Linked paired strand sequencing

ABSTRACT

Provided herein are methods for sequencing both strands of a double stranded nucleic acid fragment that improves fidelity and accuracy of a sequence determination compared to traditional next generation sequencing methods. Compositions and kits for use in the methods are also provided.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.62/986,527, filed Mar. 6, 2020; U.S. Provisional Application No.63/020,881, filed May 6, 2020; and U.S. Provisional Application No.63/087,125, filed Oct. 2, 2020; which are incorporated herein byreference in their entirety and for all purposes.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Mar. 4, 2021, isnamed 051385-523001US_SL_ST25.txt and is 5,134 bytes in size.

BACKGROUND

DNA sequencing is a fundamental tool in biological and medical research;it is an essential technology for the paradigm of personalized precisionmedicine. Sanger sequencing, where the sequence of a nucleic acid isdetermined by selective incorporation and detection ofdideoxynucleotides, enabled the mapping of the first human referencegenome. While this methodology is still useful for validating newersequencing technologies, efforts to sequence and assemble genomes usingthe Sanger method are an expensive and laborious undertaking, requiringspecialized equipment and expertise. Next generation sequencing (NGS)methodologies make use of simultaneously sequencing millions offragments of nucleic acids in a single run. However, traditional NGSstruggles with distinguishing rare sequence variants from errorsintroduced during sample preparation, amplification, and/or sequencing.

SUMMARY

In view of the foregoing, innovative approaches to address issues withexisting sequencing technologies are needed. Disclosed herein aresolutions to these and other problems in the art which, in embodiments,increase the fidelity and accuracy of high throughput sequencingmethods. In certain embodiments, the compositions and methods providedherein reduce the amount of nucleic acid manipulation and duplicationrequired by traditional next generation sequencing techniques. Inembodiments, the sequencing methods described herein permit greateraccuracy of a sequence determination compared to traditional nextgeneration sequencing methods without requiring additional sequencingdepth.

In some aspects, presented herein is a method of sequencing a doublestranded nucleic acid. In embodiments, the method comprises (a) ligatinga first adapter to a first end of the double stranded nucleic acid, andligating a second adapter to a second end of the double stranded nucleicacid, wherein the second adapter is a hairpin adapter, thereby forming anucleic acid template; (b) annealing a first primer to the nucleic acidtemplate, wherein the first primer comprises a sequence that iscomplementary to a portion of the first adapter, or a complementthereof; (c) sequencing a first portion of the nucleic acid template byextending the first primer, thereby generating a first read (andgenerating an extended sequencing primer) comprising a first nucleicacid sequence of at least a first portion of the double stranded nucleicacid; (d) annealing a second primer to the nucleic acid template,wherein the second primer comprises a sequence that is complementary toa sequence within a loop or stem of the hairpin adapter, or a complementthereof; and (e) sequencing a second portion of the nucleic acidtemplate by extending the second primer, thereby generating a secondread (and generating an extended sequencing primer) comprising a nucleicacid sequence of at least a second portion of the double strandednucleic acid. In some embodiments, the double stranded nucleic acidcomprises a forward strand and a reverse strand.

In some embodiments, the first adapter is a Y-adapter. In someembodiments, the Y-adapter comprises (i) a first strand having a 5′-armand a 3′-portion, and (ii) a second strand having a 5′-portion and a3′-arm, wherein the 3′-portion of the first strand is substantiallycomplementary to the 5′-portion of the second strand, and the 5′-arm ofthe first strand is not substantially complementary to the 3′-arm of thesecond strand. In some embodiments, the ligating of the first adaptercomprises ligating a 3′-end of the first strand of the Y-adapter to a5′-end of the forward strand of the double stranded nucleic acid, andligating a 5′-end of the second strand of the Y-adapter to a 3′-end ofthe reverse strand of the double stranded nucleic acid. In someembodiments, the first primer anneals to the second strand of theY-adapter. In some embodiments, the 5′-arm of the first strand or the3′-arm of the second strand of the Y-adapter comprises a GC content ofgreater than 50%. In some embodiments, the 5′-arm of the first strand orthe 3′-arm of the second strand of the Y-adapter comprises a meltingtemperature (Tm) in a range of 60-85° C. In certain embodiments, the5′-arm of the first strand or the 3′-arm of the second strand of theY-adapter comprises modified nucleotides (e.g., locked nucleotides(i.e., LNAs) or diamino purine nucleotides). In some embodiments, the3′-portion of the first strand or the 5′-portion of second strand of theY-adapter comprises a Tm in a range of about 40-50° C. In someembodiments, a duplex comprising the 3′-portion of the first strand andthe 5′-portion of second strand of the Y-adapter comprise a Tm of lessthan 40° C. In some embodiments, a duplex comprising the 3′-portion ofthe first strand and the 5′-portion of second strand of the Y-adaptercomprise a Tm of about 30° C., 32° C., 34° C., 36° C., 38° C., or 40° C.In some embodiments, a duplex comprising the 3′-portion of the firststrand and the 5′-portion of second strand of the Y-adapter comprise aTm in a range of 40-50° C. In some embodiments, the 3′-end or 3′-arm ofthe second strand of the Y-adapter comprises a binding motif or anucleic acid sequence complementary to a capture nucleic acid. In someembodiments, the 5′-end or 5′-arm of the first strand of the Y-adaptercomprises a binding motif or a nucleic acid sequence substantiallyidentical to a capture nucleic acid. In some embodiments, a nucleic acidtemplate generated by a method herein comprises sequences of the firststrand of a Y-adapter, a forward strand of a double stranded nucleicacid, a second adapter, a reverse strand of the double stranded nucleicacid and a second strand of the Y-adapter arranged in a 5′ to 3′direction. In some embodiments, a first primer anneals to a 5′-portionof the second strand of the Y-adapter. In embodiments, about 6, 8, 10,12, or 14 nucleotides of the 3′-portion of the first strand and the5′-portion of the second strand are substantially complementary. Inembodiments, about 10 to 12 nucleotides of the 3′-portion of the firststrand and the 5′-portion of the second strand are substantiallycomplementary.

In some embodiments, a first adapter is a hairpin adapter. In someembodiments, a first primer anneals to a sequence within a loop of thefirst adapter.

In some embodiments, the first read comprises a nucleic acid sequence ofthe reverse strand of the double stranded nucleic acid, or a portionthereof, and the second read comprises a nucleic acid sequence of theforward strand of the double stranded nucleic acid, or a portionthereof. In some embodiments, the first read comprises a nucleic acidsequence of the forward strand of the double stranded nucleic acid, or aportion thereof, and the second read comprises a nucleic acid sequenceof the reverse strand of the double stranded nucleic acid, or a portionthereof.

In some embodiments, the second adapter is a hairpin adapter comprisinga nucleic acid having a 5′-end, a 5′-portion, a loop, a 3′-portion and a3′-end, and the 5′-portion of the second adapter is substantiallycomplementary to the 3′-portion of the second adapter. In someembodiments, ligating of the second adapter comprises ligating the5′-end of the second adapter to a 3′-end of the forward strand of adouble stranded nucleic acid and ligating the 3′-end of the secondadapter to a 5′-end of the reverse strand of the double stranded nucleicacid. In some embodiments, a duplex comprising the 5′-portion and the3′-portion of the second adapter comprise a Tm in a range of 40-50° C.In some embodiments, a duplex comprising the 5′-portion and the3′-portion of the second adapter comprise a Tm in a range of about40-50° C. In some embodiments, a duplex comprising the 5′-portion andthe 3′-portion of the second adapter comprise a Tm of less than 40° C.In some embodiments, a duplex comprising the 5′-portion and the3′-portion of the second adapter comprise a Tm of about 30° C., 32° C.,34° C., 36° C., 38° C., or 40° C.

In some embodiments, the first end of the double stranded nucleic acidcomprises a blunt end, a 5′ overhang, or a 3′ overhang. In someembodiments, the second end of the double stranded nucleic acidcomprises a blunt end, a 5′ overhang, or a 3′ overhang.

In some embodiments, the method comprises generating amplicons of anucleic acid template described herein (e.g., the nucleic acid ligatedto a first and second adapter, as described herein). In someembodiments, the method of generating amplicons of the nucleic acidtemplate comprises a polymerase chain reaction. In some embodiments, apolymerase chain reaction comprises a bridge amplification method. Insome embodiments, generating of amplicons comprises attaching thenucleic acid template to a substrate. In some embodiments, a substratecomprises a chip, a wafer, a bead, or a flow cell. In embodiments asubstrate comprises a first capture nucleic acid comprising a nucleicacid sequence complementary to at least a portion of the second strandof the Y-adapter, or a complement thereof. In some embodiments,attaching of the nucleic acid template to the substrate comprisesannealing the nucleic acid template to the first capture nucleic acid.In some embodiments, a substrate comprises a second capture nucleic acidcomprising a nucleic acid sequence complementary to at least a portionof the first strand of the Y-adapter, or complement thereof. In someembodiments, amplicons comprise a first copy of the nucleic acidtemplate having a nucleic acid sequence that is substantially identicalto the nucleic acid sequence of the nucleic acid template, or a portionthereof, and a second copy of the template comprises a nucleic acidsequence that is substantially complementary to the nucleic acidsequence of the nucleic acid template. In some embodiments, aftergenerating the amplicons of the nucleic acid template, the first or thesecond copy of the nucleic acid template is removed from the substrate.In some embodiments, the amplicons that are attached to the substrateare attached at addressable locations on the substrate.

In embodiments where the first adapter is a hairpin adapter and thesecond adapter is a hairpin adapter, the generating of amplicons maycomprise a rolling circle amplification. In some embodiments, a methodof sequencing a template comprises a process comprising sequencing bysynthesis. In some embodiments, a first adapter and/or a second adaptercomprise one or more of a sample barcode sequence, a molecularidentifier sequence, or both.

In some aspects, presented herein is a composition for sequencing adouble stranded nucleic acid. In embodiments, the kit comprises aforward strand and a reverse strand, the composition comprising: (i) atemplate nucleic acid comprising sequences of a first strand of aY-adapter, the forward strand of the double stranded nucleic acid, ahairpin adapter, the reverse strand of the double stranded nucleic acidand a second strand of the Y-adapter arranged in a 5′ to 3′ direction;and (ii) a primer hybridized to a loop of the hairpin adapter; whereinthe template is attached to a substrate.

In some aspects, presented herein is a kit for sequencing a doublestranded nucleic acid. In embodiments, the kit comprises: (i) a firstadapter, wherein the first adapter comprises a double-stranded portionand at least one single-stranded portion; (ii) a second adapter, whereinthe second adapter is a hairpin adapter comprising a nucleic acid havinga 5′-end, a 5′-portion, a loop, a 3′-portion and a 3′-end, and the5′-portion of the hairpin adapter is substantially complementary to the3′-portion of the hairpin adapter; (iii) a first primer having a nucleicacid sequence complementary to a portion of the first adapter, or acomplement thereof and (iv) a second primer having a nucleic acidsequence complementary to the loop of the hairpin adapter, or acomplement thereof. In some embodiments, the first adapter is aY-adapter, where the Y-adapter comprises (i) a first strand having a5′-arm and a 3′-portion, and (ii) a second strand having a 5′-portionand a 3′-arm, wherein the 3′-portion of the first strand issubstantially complementary to the 5′-portion of the second strand, andthe 5′-arm is not substantially complementary to the 3′-arm. In someembodiments, the first adapter is a hairpin adapter.

In some aspects, presented herein is a method of selectively sequencinga double-stranded nucleic acid. In embodiments, the method comprises (a)ligating a first adapter to a first end of the double-stranded nucleicacid, and ligating a second adapter to a second end of thedouble-stranded nucleic acid, wherein the second adapter is a hairpinadapter; (b) displacing at least a portion of one strand of thedouble-stranded nucleic acid from step (a); (c) hybridizing a probeoligonucleotide to the displaced portion of the double-stranded nucleicacid; (d) separating the probe-hybridized double-stranded nucleic acidfrom nucleic acids not hybridized to a probe; and (e) sequencing theprobe-hybridized double-stranded nucleic acid of step (d).

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1D. FIG. 1A shows an embodiment of an adapter-target-adaptertemplate comprising a double stranded nucleic acid of interest annealedto a Y-adapter and a hairpin adapter. FIG. 1B shows an embodiment of anadapter ligation process where a hairpin adapter may comprise anoptional UMI (unique molecular identifier; barcode). FIG. 1C shows anembodiment of an adapter-target-adapter template where a double strandednucleic acid of interest is annealed to a first hairpin adapter (hairpinadapter 1) and a second, non-identical, hairpin adapter (hairpin adapter2). FIG. 1D shows an embodiment of an adapter ligation process.

FIGS. 2A-2B show embodiments of an adapter. FIG. 2A shows an embodimentof a Y adapter. FIG. 2B shows an embodiment of a hairpin adaptercomprising a 5′-end, a 5′ portion, a loop, a 3′ portion and a 3′-end. Inthis embodiment, a duplex region of the adapter comprises a Tm (meltingtemperature) of about 40-45° C. and a length of about 10-16 bases. Inembodiments, the duplex region of the adapter comprises a Tm (meltingtemperature) of about 35-45° C. or 30-45° C. and a length of about 12bases.

FIG. 3 shows embodiments of a Y adapter. In some embodiments, a Yadapter is double stranded at one end (the double-stranded region) andsingle stranded at the other end (the unmatched region), wherein 5′Prefers to a phosphorylated 5′ end. The double-stranded region of a Yadapter (alternatively referred to as a forked adapter) may beblunt-ended (top), have a 3′ overhang (middle), or a 5′ overhang(bottom). An overhang may comprise a single nucleotide or more than onenucleotide.

FIG. 4 shows an embodiment of a hairpin adapter, which includes a doublestranded (stem) region and a loop region. Within the loop region is apriming site (P3) and optionally a unique molecular identifier.

FIG. 5 shows embodiments of hairpin adapters, each comprising a 5′-endand a 3′-end. In some embodiments, a hairpin adapter comprises a doublestranded portion (a double-stranded “stem” region) and a loop, where 5′Prefers to a phosphorylated 5′ end. A double-stranded stem region of ahairpin adapter may be blunt-ended (top), it may have a 5′ overhang(middle), or a 3′ overhang (bottom). An overhang may comprise a singlenucleotide or more than one nucleotide.

FIGS. 6A-6B show an overview of an embodiment of an amplificationmethod. FIG. 6A shows a Y-template-hairpin construct hybridizing to animmobilized P2 primer. In the presence of a polymerase, a copy of theoriginal template is made; this copy then hybridizes to an immobilizedP1 primer. FIG. 6B depicts annealing, extending, denaturing,re-annealing, and extending steps common to one embodiment of anamplification method described herein.

FIGS. 7A-7B show an overview of an embodiment of a linked duplexsequencing process; the gray ellipse represents a polymerase. FIG. 7Ashows a process where a template bound to an immobilized P1 isoptionally cleaved at X and removed. The P2-anchored strands areterminated using a suitable technique (e.g., depicted is adideoxynucleotide (dd), however any suitable terminating process iscontemplated herein). FIG. 7B shows sequencing up with a stranddisplacing polymerase (left), following by priming at the P3 primingsite and sequencing down with a strand displacing polymerase (right).

FIG. 8 shows an overview of an embodiment of a seeding and amplificationprocess, wherein the amplification method includes rolling circleamplification (RCA), exponential rolling circle amplification (eRCA), ora method of amplification which includes PCR and RCA or PCR and eRCA.

FIG. 9 shows an overview of an embodiment of an affinity capture processof a Y-template-hairpin construct by hybridization with a capture probe,wherein the capture probe is a biotinylated capture probe.

FIG. 10 shows an overview of an embodiment of an affinity captureprocess for a Y-template-hairpin construct comprising a modificationwithin the loop region that prevents further elongation (the “temporarystopper,” also referred to herein as a “terminating nucleotide”),thereby rendering the second strand of the construct available forcapture.

FIG. 11 shows an overview of an embodiment of an affinity captureprocess for a Y-hairpin construct in which a primer is complementary toa region within the loop of the hairpin adapter of the construct. Theresult of primer elongation is a double stranded second strand of theY-hairpin construct, and a single stranded first strand which remainsavailable for capture.

FIG. 12 shows an overview of an embodiment of an affinity captureprocess of a Y-hairpin construct in which a primer invades the doublestranded region of the hairpin adapter of the construct upstream of thesecond strand of the construct, via the use of a recombinase and of aloading factor. Elongation of the primer results in a double strandedsecond strand, and a single stranded first strand which remainsavailable for capture.

FIG. 13 shows an overview of an embodiment of an affinity captureprocess of a Y-hairpin construct in which a biotinylated invasioncapture probe is bound to a target sequence of the construct via the useof a recombinase and of a loading factor.

FIGS. 14A-14C show an overview of an embodiment of on-surface sequentialligation of a DNA template for sequencing, as described in Example 8.Depicted in FIG. 14A (right side), the target DNA is double stranded andcontains a 5′ phosphate for ligation. The loop of the hairpin adapterincludes a priming region (PR), depicted in FIG. 14A as P3. The loop ofthe hairpin adapter may include an optional UMI (unique molecularidentifier; barcode). To circularize the ds template DNA, a firsthairpin adapter is hybridized to a surface-immobilized oligos, referredto as P3′ in FIGS. 14A-14B. The target DNA is ligated to the hairpinadapter to form an adapter duplex. A second hairpin adapter isintroduced and ligated to the adapter-duplex to form a circularizedproduct, wherein the second hairpin adapter includes a different PR(i.e., P1 and P2 as illustrated) than the first hairpin adapter (seeFIG. 14B). Alternatively, as shown in FIG. 14C, a Y-adapter isintroduced, depicted as P1 and P2 in FIG. 14C, and ligated to theadapter-duplex to form an adapter-target-adapter construct resembling abobby-pin structure.

FIGS. 15A-15D show an overview of an embodiment of an amplificationmethod for linked methylation detection of a cytosine-convertedadapter-target-adapter construct. FIG. 15A shows a Y-template-hairpinconstruct containing methylated cytosines undergoing cytosineconversion. Cytosines lacking a methyl group are converted to uracil.Following bisulfite conversion, adapter-target-adapter constructs may beamplified prior to clustering. FIG. 15B shows a cytosine-convertedY-template-hairpin construct hybridizing to an immobilized P2 primer. Inthe presence of a polymerase, a copy of the original template is made;this copy then hybridizes to an immobilized P1 primer. The uracil iscopied as an adenine, while the Me-C are copied as guanines. FIG. 15Cdepicts annealing, extending, denaturing, re-annealing, and extendingsteps common to one embodiment of an amplification method for acytosine-converted construct. FIG. 15D shows an amplified,cytosine-converted Y-template-hairpin construct hybridizing to animmobilized P2 primer. As this was amplified prior to hybridization, theuracil has now been replaced with a thymine. In the presence of apolymerase, a copy of the original template is made; this copy thenhybridizes to an immobilized P1 primer as shown in FIG. 15C.

FIG. 16 illustrates an overview of an exemplary workflow for analysis ofhemimethylated DNA (e.g., asymmetric methylation methods as describedherein). First, to a cfDNA sample, a first adapter is ligated to a firstend of the cfDNA molecule, and a second adapter is ligated to a secondend of the cfDNA molecule, wherein the second adapter is a hairpinadapter, thereby forming a nucleic acid template. Following ligation thesample may be optionally captured via a target capture (e.g., ahybridization capture panel), subjected to cytosine conversion (e.g.,bisulfite conversion or an enzymatic conversion method), amplified,followed by sequencing to identify hemimethylated DNA fragments.Sequencing reads representing hemimethylated fragments are then used fordownstream analysis, for example via mapping to a reference genome toidentify hemimethylated DNA regions to assess patterns of cytosinemethylation on both strands.

FIGS. 17A-17B. FIG. 17A Illustrates an embodiment of the Y-templateadapter containing a bisulfite conversion control region consisting ofone or more unmethylated cytosine bases. Following bisulfite treatment,the efficiency of bisulfite conversion may be estimated via the fractionof cytosine bases within this region that are read as thymine. Anoptional methylcytosine UMI region is located adjacent to the bisulfiteconversion control region. This element consists of a plurality ofcytosine bases designed to be methylated with approximately 50%probability, such that bisulfite conversion gives rise to a lowcomplexity UMI consisting of the resultant combination of methylationprotected (unconverted) and bisulfite converted bases. Optionally, thedouble stranded stem region of the adapter may be designed to containone or more unmethylated cytosines, which reduce self-complementarity ofthe construct following bisulfite conversion. In embodiments, the one ormore unmethylated cytosines are not present in the sequence that iscomplementary to a sequencing primer. FIG. 17B Illustrates an embodimentof the hairpin adapter containing an optional bisulfite conversioncontrol region, an optional methylcytosine UMI region, and optionallyincluding unmethylated cytosines within the stem region to reduceself-complementarity following bisulfite conversion.

FIGS. 18A-18B. An illustration depicting generating a blocking strand toallow for sequencing two strands of a template nucleic acid. FIG. 18Ashows a Y-template-hairpin construct attached to the solid support. Aprimer anneals to the loop of the hairpin (identified as P3 in FIG. 18A)and is extended with a strand displacing enzyme (depicted as a grayellipse). A sequencing primer hybridizes to the liberated end of theconstruct and is extended in the presence of a sequencing enzyme togenerate a first sequencing read, as shown in FIG. 18B. The hairpin mayinclude a cleavable site, depicted as an ‘X’, and may optionally becleaved and removed. A second sequencing primer is then annealed to the3′ end of the immobilized single-stranded template, and is sequenced inthe presence of a sequencing enzyme to generate a second sequencingread.

FIGS. 19A-19D show an overview of an embodiment of an amplificationmethod for true somatic variant detection of an oxidativedamage-containing (e.g., 8-oxo-dG) adapter-target-adapter construct.FIG. 19A shows an 8-oxo-dG-containing Y-template-hairpin constructhybridizing to an immobilized P2 primer. In the presence of apolymerase, a copy of the original template is made; this copy thenhybridizes to an immobilized P1 primer. The 8-oxo-dG is copied as anadenine, resulting in an A-G mismatch. FIG. 19B depicts annealing,extending, denaturing, re-annealing, and extending steps common to oneembodiment of an amplification method for an oxidative damage-inducedconstruct. Boxes have been drawn to highlight mismatches. FIG. 19C showsa Y-template-hairpin construct containing an 8-oxo-dG base undergoingamplification. Following amplification, the damaged base is replacedwith a thymine. FIG. 19D shows hybridization of the amplifiedY-template-hairpin construct of FIG. 19C to an immobilized P2 primer. Inthe presence of a polymerase, a copy of the template is made; this copythen hybridizes to an immobilized P1 primer as shown in FIG. 19B.

FIG. 20. A plot showing an example average error rate (ErrorRate=1−Accuracy) per sequencing cycle. The first sequencing read(circles, top plot) shows the sequencing error as a function of cyclenumber from the first strand (Read 1). The corrected read (triangles,bottom plot) shows the sequencing error when read 1 reads arebioinformatically corrected based on the combined weight of the secondstrand (Read 2) sequencing reads. Base calling accuracy, measured by thePhred quality score (Q score), is the most common metric used to assessthe accuracy of a sequencing platform. It indicates the probability thata given base is called incorrectly by the sequencer. For example, if thebase calling algorithm assigns a Q score of 30 (Q30) to a base, this isequivalent to the probability of an incorrect base call 1 in 1000 times.This means that the base call accuracy (i.e., the probability of acorrect base call) is 99.9%. In some embodiments, methods describedherein permit a double pass rate to be at least double the single-passrate, i.e., 10⁻⁶ (Q60).

DETAILED DESCRIPTION I. Definitions

The practice of the technology described herein will employ, unlessindicated specifically to the contrary, conventional methods ofchemistry, biochemistry, organic chemistry, molecular biology,microbiology, recombinant DNA techniques, genetics, immunology, and cellbiology that are within the skill of the art, many of which aredescribed below for the purpose of illustration. Examples of suchtechniques are available in the literature. Methods, devices andmaterials similar or equivalent to those described herein can be used inthe practice of embodiments of the present invention.

All patents, patent applications, articles and publications mentionedherein, both supra and infra, are hereby expressly incorporated hereinby reference in their entireties.

Unless defined otherwise herein, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this disclosure belongs. Various scientificdictionaries that include the terms included herein are well known andavailable to those in the art. Although any methods and materialssimilar or equivalent to those described herein find use in the practiceor testing of the disclosure, some preferred methods and materials aredescribed. Accordingly, the terms defined immediately below are morefully described by reference to the specification as a whole. It is tobe understood that this disclosure is not limited to the particularmethodology, protocols, and reagents described, as these may vary,depending upon the context in which they are used by those of skill inthe art. The following definitions are provided to facilitateunderstanding of certain terms used frequently herein and are not meantto limit the scope of the present disclosure.

As used herein, the singular terms “a”, “an”, and “the” include theplural reference unless the context clearly indicates otherwise.Reference throughout this specification to, for example, “oneembodiment”, “an embodiment”, “another embodiment”, “some embodiments”,“a particular embodiment”, “a related embodiment”, “a certainembodiment”, “an additional embodiment”, or “a further embodiment” orcombinations thereof means that a particular feature, structure orcharacteristic described in connection with the embodiment is includedin at least one embodiment of the present disclosure. Thus, theappearances of the foregoing phrases in various places throughout thisspecification are not necessarily all referring to the same embodiment.Furthermore, the particular features, structures, or characteristics maybe combined in any suitable manner in one or more embodiments.

As used herein, the term “about” means a range of values including thespecified value, which a person of ordinary skill in the art wouldconsider reasonably similar to the specified value. In embodiments, theterm “about” means within a standard deviation using measurementsgenerally acceptable in the art. In embodiments, about means a rangeextending to +/−10% of the specified value. In embodiments, about meansthe specified value.

Throughout this specification, unless the context requires otherwise,the words “comprise”, “comprises” and “comprising” will be understood toimply the inclusion of a stated step or element or group of steps orelements but not the exclusion of any other step or element or group ofsteps or elements. By “consisting of” is meant including, and limitedto, whatever follows the phrase “consisting of” Thus, the phrase“consisting of” indicates that the listed elements are required ormandatory, and that no other elements may be present. By “consistingessentially of” is meant including any elements listed after the phrase,and limited to other elements that do not interfere with or contributeto the activity or action specified in the disclosure for the listedelements. Thus, the phrase “consisting essentially of” indicates thatthe listed elements are required or mandatory, but that other elementsare optional and may or may not be present depending upon whether or notthey affect the activity or action of the listed elements.

As used herein, the term “control” or “control experiment” is used inaccordance with its plain and ordinary meaning and refers to anexperiment in which the subjects or reagents of the experiment aretreated as in a parallel experiment except for omission of a procedure,reagent, or variable of the experiment. In some instances, the controlis used as a standard of comparison in evaluating experimental effects.

As used herein, the term “complement” is used in accordance with itsplain and ordinary meaning and refers to a nucleotide (e.g., RNAnucleotide or DNA nucleotide) or a sequence of nucleotides capable ofbase pairing with a complementary nucleotide or sequence of nucleotides(e.g., Watson-Crick base pairing). As described herein and commonlyknown in the art the complementary (matching) nucleotide of adenosine isthymidine and the complementary (matching) nucleotide of guanosine iscytosine. Thus, a complement may include a sequence of nucleotides thatbase paired with corresponding complementary nucleotides of a secondnucleic acid sequence. The nucleotides of a complement may partially orcompletely match the nucleotides of the second nucleic acid sequence.Where the nucleotides of the complement completely match each nucleotideof the second nucleic acid sequence, the complement forms base pairswith each nucleotide of the second nucleic acid sequence. Where thenucleotides of the complement partially match the nucleotides of thesecond nucleic acid sequence only some of the nucleotides of thecomplement form base pairs with nucleotides of the second nucleic acidsequence. Examples of complementary sequences include coding andnon-coding sequences, wherein the non-coding sequence containscomplementary nucleotides to the coding sequence and thus forms thecomplement of the coding sequence. A further example of complementarysequences are sense and antisense sequences, wherein the sense sequencecontains complementary nucleotides to the antisense sequence and thusforms the complement of the antisense sequence.

As described herein, the complementarity of sequences may be partial, inwhich only some of the nucleic acids match according to base pairing, orcomplete, where all the nucleic acids match according to base pairing.Thus, two sequences that are complementary to each other, may have aspecified percentage of nucleotides that complement one another (e.g.,about 60%, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99%, or higher complementarity over a specifiedregion). In embodiments, two sequences are complementary when they arecompletely complementary, having 100% complementarity. In embodiments,sequences in a pair of complementary sequences form portions of a singlepolynucleotide with non-base-pairing nucleotides (e.g., as in a hairpinor loop structure, with or without an overhang) or portions of separatepolynucleotides. In embodiments, one or both sequences in a pair ofcomplementary sequences form portions of longer polynucleotides, whichmay or may not include additional regions of complementarity.

As used herein, the term “contacting” is used in accordance with itsplain ordinary meaning and refers to the process of allowing at leasttwo distinct species (e.g. chemical compounds including biomolecules orcells) to become sufficiently proximal to react, interact or physicallytouch. However, the resulting reaction product can be produced directlyfrom a reaction between the added reagents or from an intermediate fromone or more of the added reagents that can be produced in the reactionmixture. The term “contacting” may include allowing two species toreact, interact, or physically touch, wherein the two species may be acompound, a protein or enzyme (e.g., a DNA polymerase).

As may be used herein, the terms “nucleic acid,” “nucleic acidmolecule,” “nucleic acid sequence,” “nucleic acid fragment” and“polynucleotide” are used interchangeably and are intended to include,but are not limited to, a polymeric form of nucleotides covalentlylinked together that may have various lengths, eitherdeoxyribonucleotides or ribonucleotides, or analogs, derivatives ormodifications thereof. Different polynucleotides may have differentthree-dimensional structures, and may perform various functions, knownor unknown. Non-limiting examples of polynucleotides include a gene, agene fragment, an exon, an intron, intergenic DNA (including, withoutlimitation, heterochromatic DNA), messenger RNA (mRNA), transfer RNA,ribosomal RNA, a ribozyme, cDNA, a recombinant polynucleotide, abranched polynucleotide, a plasmid, a vector, isolated DNA of asequence, isolated RNA of a sequence, a nucleic acid probe, and aprimer. Polynucleotides useful in the methods of the disclosure maycomprise natural nucleic acid sequences and variants thereof, artificialnucleic acid sequences, or a combination of such sequences. As may beused herein, the terms “nucleic acid oligomer” and “oligonucleotide” areused interchangeably and are intended to include, but are not limitedto, nucleic acids having a length of 200 nucleotides or less. In someembodiments, an oligonucleotide is a nucleic acid having a length of 2to 200 nucleotides, 2 to 150 nucleotides, 5 to 150 nucleotides or 5 to100 nucleotides. In some embodiments, an oligonucleotide is a primerconfigured for extension by a polymerase when the primer is annealedcompletely or partially to a complementary nucleic acid template. Aprimer is often a single stranded nucleic acid. In certain embodiments,a primer, or portion thereof, is substantially complementary to aportion of an adapter. In some embodiments, a primer has a length of 200nucleotides or less. In certain embodiments, a primer has a length of 10to 150 nucleotides, 15 to 150 nucleotides, 5 to 100 nucleotides, 5 to 50nucleotides or 10 to 50 nucleotides.

As used herein, the terms “polynucleotide primer” and “primer” refers toany polynucleotide molecule that may hybridize to a polynucleotidetemplate, be bound by a polymerase, and be extended in atemplate-directed process for nucleic acid synthesis. The primer may bea separate polynucleotide from the polynucleotide template, or both maybe portions of the same polynucleotide (e.g., as in a hairpin structurehaving a 3′ end that is extended along another portion of thepolynucleotide to extend a double-stranded portion of the hairpin).Primers (e.g., forward or reverse primers) may be attached to a solidsupport. A primer can be of any length depending on the particulartechnique it will be used for. For example, PCR primers are generallybetween 10 and 40 nucleotides in length. The length and complexity ofthe nucleic acid fixed onto the nucleic acid template may vary. In someembodiments, a primer has a length of 200 nucleotides or less. Incertain embodiments, a primer has a length of 10 to 150 nucleotides, 15to 150 nucleotides, 5 to 100 nucleotides, 5 to 50 nucleotides or 10 to50 nucleotides. One of skill can adjust these factors to provide optimumhybridization and signal production for a given hybridization procedure.The primer permits the addition of a nucleotide residue thereto, oroligonucleotide or polynucleotide synthesis therefrom, under suitableconditions. In an embodiment the primer is a DNA primer, i.e., a primerconsisting of, or largely consisting of, deoxyribonucleotide residues.The primers are designed to have a sequence that is the complement of aregion of template/target DNA to which the primer hybridizes. Theaddition of a nucleotide residue to the 3′ end of a primer by formationof a phosphodiester bond results in a DNA extension product. Theaddition of a nucleotide residue to the 3′ end of the DNA extensionproduct by formation of a phosphodiester bond results in a further DNAextension product. In another embodiment the primer is an RNA primer. Inembodiments, a primer is hybridized to a target polynucleotide. A“primer” is complementary to a polynucleotide template, and complexes byhydrogen bonding or hybridization with the template to give aprimer/template complex for initiation of synthesis by a polymerase,which is extended by the addition of covalently bonded bases linked atits 3′ end complementary to the template in the process of DNAsynthesis.

In some embodiments, a nucleic acid comprises a capture nucleic acid. Acapture nucleic acid refers to a nucleic acid that is attached to asubstrate. In some embodiments, a capture nucleic acid comprises aprimer. In some embodiments, a capture nucleic acid is a nucleic acidconfigured to specifically hybridize to a portion of one or more nucleicacid templates (e.g., a template of a library). In some embodiments acapture nucleic acid configured to specifically hybridize to a portionof one or more nucleic acid templates is substantially complementary toa suitable portion of a nucleic acid template, or an amplicon thereof.In some embodiments a capture nucleic acid is configured to specificallyhybridize to a portion of an adapter, or a portion thereof. In someembodiments a capture nucleic acid, or portion thereof, is substantiallycomplementary to a portion of an adapter, or a complement thereof. Inembodiments, a capture nucleic acid is a probe oligonucleotide.Typically, a probe oligonucleotide is complementary to a targetpolynucleotide or portion thereof, and further comprises a label (suchas a binding moiety) or is attached to a surface, such thathybridization to the probe oligonucleotide permits the selectiveisolation of probe-bound polynucleotides from unbound polynucleotides ina population. A probe oligonucleotide may or may not also be used as aprimer.

Nucleic acids, including e.g., nucleic acids with a phosphorothioatebackbone, can include one or more reactive moieties. As used herein, theterm reactive moiety includes any group capable of reacting with anothermolecule, e.g., a nucleic acid or polypeptide through covalent,non-covalent or other interactions. By way of example, the nucleic acidcan include an amino acid reactive moiety that reacts with an amio acidon a protein or polypeptide through a covalent, non-covalent or otherinteraction.

A polynucleotide is typically composed of a specific sequence of fournucleotide bases: adenine (A); cytosine (C); guanine (G); and thymine(T) (uracil (U) for thymine (T) when the polynucleotide is RNA). Thus,the term “polynucleotide sequence” is the alphabetical representation ofa polynucleotide molecule; alternatively, the term may be applied to thepolynucleotide molecule itself. This alphabetical representation can beinput into databases in a computer having a central processing unit andused for bioinformatics applications such as functional genomics andhomology searching. Polynucleotides may optionally include one or morenon-standard nucleotide(s), nucleotide analog(s) and/or modifiednucleotides.

As used herein, the terms “analogue” and “analog”, in reference to achemical compound, refers to compound having a structure similar to thatof another one, but differing from it in respect of one or moredifferent atoms, functional groups, or substructures that are replacedwith one or more other atoms, functional groups, or substructures. Inthe context of a nucleotide, a nucleotide analog refers to a compoundthat, like the nucleotide of which it is an analog, can be incorporatedinto a nucleic acid molecule (e.g., an extension product) by a suitablepolymerase, for example, a DNA polymerase in the context of a nucleotideanalogue. The terms also encompass nucleic acids containing knownnucleotide analogs or modified backbone residues or linkages, which aresynthetic, naturally occurring, or non-naturally occurring, which havesimilar binding properties as the reference nucleic acid, and which aremetabolized in a manner similar to the reference nucleotides. Examplesof such analogs include, include, without limitation, phosphodiesterderivatives including, e.g., phosphoramidate, phosphorodiamidate,phosphorothioate (also known as phosphorothioate having double bondedsulfur replacing oxygen in the phosphate), phosphorodithioate,phosphonocarboxylic acids, phosphonocarboxylates, phosphonoacetic acid,phosphonoformic acid, methyl phosphonate, boron phosphonate, orO-methylphosphoroamidite linkages (see, e.g., see Eckstein,OLIGONUCLEOTIDES AND ANALOGUES: A PRACTICAL APPROACH, Oxford UniversityPress) as well as modifications to the nucleotide bases such as in5-methyl cytidine or pseudouridine; and peptide nucleic acid backbonesand linkages. Other analog nucleic acids include those with positivebackbones; non-ionic backbones, modified sugars, and non-ribosebackbones (e.g. phosphorodiamidate morpholino oligos or locked nucleicacids (LNA)), including those described in U.S. Pat. Nos. 5,235,033 and5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, CARBOHYDRATEMODIFICATIONS IN ANTISENSE RESEARCH, Sanghui & Cook, eds. Nucleic acidscontaining one or more carbocyclic sugars are also included within onedefinition of nucleic acids. Modifications of the ribose-phosphatebackbone may be done for a variety of reasons, e.g., to increase thestability and half-life of such molecules in physiological environmentsor as probes on a biochip. Mixtures of naturally occurring nucleic acidsand analogs can be made; alternatively, mixtures of different nucleicacid analogs, and mixtures of naturally occurring nucleic acids andanalogs may be made. In embodiments, the internucleotide linkages in DNAare phosphodiester, phosphodiester derivatives, or a combination ofboth.

As used herein, a “native” nucleotide is used in accordance with itsplain and ordinary meaning and refers to a naturally occurringnucleotide that does not include an exogenous label (e.g., a fluorescentdye, or other label) or chemical modification such as may characterize anucleotide analog. Examples of native nucleotides useful for carryingout procedures described herein include: dATP(2′-deoxyadenosine-5′-triphosphate); dGTP(2′-deoxyguanosine-5′-triphosphate); dCTP(2′-deoxycytidine-5′-triphosphate); dTTP(2′-deoxythymidine-5′-triphosphate); and dUTP(2′-deoxyuridine-5′-triphosphate).

In embodiments, the nucleotides of the present disclosure use acleavable linker to attach the label to the nucleotide. The use of acleavable linker ensures that the label can, if required, be removedafter detection, avoiding any interfering signal with any labellednucleotide incorporated subsequently. The use of the term “cleavablelinker” is not meant to imply that the whole linker is required to beremoved from the nucleotide base. The cleavage site can be located at aposition on the linker that ensures that part of the linker remainsattached to the nucleotide base after cleavage. The linker can beattached at any position on the nucleotide base provided thatWatson-Crick base pairing can still be carried out. In the context ofpurine bases, it is preferred if the linker is attached via the7-position of the purine or the preferred deazapurine analogue, via an8-modified purine, via an N-6 modified adenosine or an N-2 modifiedguanine. For pyrimidines, attachment is preferably via the 5-position oncytidine, thymidine or uracil and the N-4 position on cytosine. The term“cleavable linker” or “cleavable moiety” as used herein refers to adivalent or monovalent, respectively, moiety which is capable of beingseparated (e.g., detached, split, disconnected, hydrolyzed, a stablebond within the moiety is broken) into distinct entities. A cleavablelinker is cleavable (e.g., specifically cleavable) in response toexternal stimuli (e.g., enzymes, nucleophilic/basic reagents, reducingagents, photo-irradiation, electrophilic/acidic reagents, organometallicand metal reagents, or oxidizing reagents). A chemically cleavablelinker refers to a linker which is capable of being split in response tothe presence of a chemical (e.g., acid, base, oxidizing agent, reducingagent, Pd(0), tris-(2-carboxyethyl)phosphine, dilute nitrous acid,fluoride, tris(3-hydroxypropyl)phosphine), sodium dithionite (Na₂S₂O₄),or hydrazine (N₂H₄)). A chemically cleavable linker is non-enzymaticallycleavable. In embodiments, the cleavable linker is cleaved by contactingthe cleavable linker with a cleaving agent. In embodiments, the cleavingagent is a phosphine containing reagent (e.g., TCEP or THPP), sodiumdithionite (Na₂S₂O₄), weak acid, hydrazine (N₂H₄), Pd(0), orlight-irradiation (e.g., ultraviolet radiation).

As used herein, the term “modified nucleotide” refers to nucleotidemodified in some manner. Typically, a nucleotide contains a single5-carbon sugar moiety, a single nitrogenous base moiety and 1 to threephosphate moieties. In embodiments, a nucleotide can include a blockingmoiety and/or a label moiety. A blocking moiety on a nucleotide preventsformation of a covalent bond between the 3′ hydroxyl moiety of thenucleotide and the 5′ phosphate of another nucleotide. A blocking moietyon a nucleotide can be reversible, whereby the blocking moiety can beremoved or modified to allow the 3′ hydroxyl to form a covalent bondwith the 5′ phosphate of another nucleotide. A blocking moiety can beeffectively irreversible under particular conditions used in a methodset forth herein. In embodiments, the blocking moiety is attached to the3′ oxygen of the nucleotide and is independently —NH₂, —CN, —CH₃, C₂-C₆allyl (e.g., —CH₂—CH═CH₂), methoxyalkyl (e.g., —CH₂—O—CH₃), or —CH₂N₃.In embodiments, the blocking moiety is attached to the 3′ oxygen of thenucleotide and is independently

A label moiety of a nucleotide can be any moiety that allows thenucleotide to be detected, for example, using a spectroscopic method.Exemplary label moieties are fluorescent labels, mass labels,chemiluminescent labels, electrochemical labels, detectable labels andthe like. One or more of the above moieties can be absent from anucleotide used in the methods and compositions set forth herein. Forexample, a nucleotide can lack a label moiety or a blocking moiety orboth. Examples of nucleotide analogues include, without limitation,7-deaza-adenine, 7-deaza-guanine, the analogues of deoxynucleotidesshown herein, analogues in which a label is attached through a cleavablelinker to the 5-position of cytosine or thymine or to the 7-position ofdeaza-adenine or deaza-guanine, and analogues in which a small chemicalmoiety is used to cap the OH group at the 3′-position of deoxyribose.Nucleotide analogues and DNA polymerase-based DNA sequencing are alsodescribed in U.S. Pat. No. 6,664,079, which is incorporated herein byreference in its entirety for all purposes.

The terms “identical” or percent “identity,” in the context of two ormore nucleic acids or polypeptide sequences, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues or nucleotides that are the same(i.e., about 60% identity, preferably 65%, 70%, 75%, 80%, 85%, 90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over aspecified region, when compared and aligned for maximum correspondenceover a comparison window or designated region) as measured using a BLASTor BLAST 2.0 sequence comparison algorithms with default parametersdescribed below, or by manual alignment and visual inspection (see,e.g., NCBI web site http://www.ncbi.nlm.nih.gov/BLAST/ or the like).Such sequences are then said to be “substantially identical.” Thisdefinition also refers to, or may be applied to, the complement of atest sequence. The definition also includes sequences that havedeletions and/or additions, as well as those that have substitutions. Asdescribed below, the preferred algorithms can account for gaps and thelike. Preferably, identity exists over a region that is at least about25 amino acids or nucleotides in length, or more preferably over aregion that is 50-100 amino acids or nucleotides in length.

As used herein, the term “removable” group, e.g., a label or a blockinggroup or protecting group, is used in accordance with its plain andordinary meaning and refers to a chemical group that can be removed froma nucleotide analogue such that a DNA polymerase can extend the nucleicacid (e.g., a primer or extension product) by the incorporation of atleast one additional nucleotide. Removal may be by any suitable method,including enzymatic, chemical, or photolytic cleavage. Removal of aremovable group, e.g., a blocking group, does not require that theentire removable group be removed, only that a sufficient portion of itbe removed such that a DNA polymerase can extend a nucleic acid byincorporation of at least one additional nucleotide using a nucleotideor nucleotide analogue. In general, the conditions under which aremovable group is removed are compatible with a process employing theremovable group (e.g., an amplification process or sequencing process).

As used herein, the terms “blocking moiety,” “reversible blockinggroup,” “reversible terminator” and “reversible terminator moiety” areused in accordance with their plain and ordinary meanings and refer to acleavable moiety which does not interfere with incorporation of anucleotide comprising it by a polymerase (e.g., DNA polymerase, modifiedDNA polymerase), but prevents further strand extension until removed(“unblocked”). For example, a reversible terminator may refer to ablocking moiety located, for example, at the 3′ position of thenucleotide and may be a chemically cleavable moiety such as an allylgroup, an azidomethyl group or a methoxymethyl group, or may be anenzymatically cleavable group such as a phosphate ester. Suitablenucleotide blocking moieties are described in applications WO2004/018497, U.S. Pat. Nos. 7,057,026, 7,541,444, WO 96/07669, U.S. Pat.Nos. 5,763,594, 5,808,045, 5,872,244 and 6,232,465 the contents of whichare incorporated herein by reference in their entirety. The nucleotidesmay be labelled or unlabeled. They may be modified with reversibleterminators useful in methods provided herein and may be 3′-O-blockedreversible or 3′-unblocked reversible terminators. In nucleotides with3′-O-blocked reversible terminators, the blocking group may berepresented as —OR [reversible terminating (capping) group], wherein Ois the oxygen atom of the 3′-OH of the pentose and R is the blockinggroup, while the label is linked to the base, which acts as a reporterand can be cleaved. The 3′-O-blocked reversible terminators are known inthe art, and may be, for instance, a 3′-ONH₂ reversible terminator, a3′-O-allyl reversible terminator, or a 3′-O-azidomethyl reversibleterminator.

In some embodiments, a nucleic acid (e.g., an adapter or a primer)comprises a molecular identifier or a molecular barcode. As used herein,the term “molecular barcode” (which may be referred to as a “tag”, a“barcode”, a a “molecular identifier”, an “identifier sequence” or a“unique molecular identifier” (UMI)) refers to any material (e.g., anucleotide sequence, a nucleic acid molecule feature) that is capable ofdistinguishing an individual molecule in a large heterogeneouspopulation of molecules. In embodiments, a barcode is unique in a poolof barcodes that differ from one another in sequence, or is uniquelyassociated with a particular sample polynucleotide in a pool of samplepolynucleotides. In embodiments, every barcode in a pool of adapters isunique, such that sequencing reads comprising the barcode can beidentified as originating from a single sample polynucleotide moleculeon the basis of the barcode alone. In other embodiments, individualbarcode sequences may be used more than once, but adapters comprisingthe duplicate barcodes are associated with different sequences and/or indifferent combinations of barcoded adaptors, such that sequence readsmay still be uniquely distinguished as originating from a single samplepolynucleotide molecule on the basis of a barcode and adjacent sequenceinformation (e.g., sample polynucleotide sequence, and/or one or moreadjacent barcodes). In embodiments, barcodes are about or at least about5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 40, 50, 75 or more nucleotides inlength. In embodiments, barcodes are shorter than 20, 15, 10, 9, 8, 7,6, or 5 nucleotides in length. In embodiments, barcodes are about 10 toabout 50 nucleotides in length, such as about 15 to about 40 or about 20to about 30 nucleotides in length. In a pool of different barcodes,barcodes may have the same or different lengths. In general, barcodesare of sufficient length and include sequences that are sufficientlydifferent to allow the identification of sequencing reads that originatefrom the same sample polynucleotide molecule. In embodiments, eachbarcode in a plurality of barcodes differs from every other barcode inthe plurality by at least three nucleotide positions, such as at least3, 4, 5, 6, 7, 8, 9, 10, or more nucleotide positions. In someembodiments, substantially degenerate barcodes may be known as random.In some embodiments, a barcode may include a nucleic acid sequence fromwithin a pool of known sequences. In some embodiments, the barcodes maybe pre-defined.

In embodiments, a nucleic acid (e.g., an adapter or primer) comprises asample barcode. In general, a “sample barcode” is a nucleotide sequencethat is sufficiently different from other sample barcode to allow theidentification of the sample source based on sample barcode sequence(s)with which they are associated. In embodiments, a plurality ofnucleotides (e.g., all nucleotides from a particular sample source, orsub-sample thereof) are joined to a first sample barcode, while adifferent plurality of nucleotides (e.g., all nucleotides from adifferent sample source, or different subsample) are joined to a secondsample barcode, thereby associating each plurality of polynucleotideswith a different sample barcode indicative of sample source. Inembodiments, each sample barcode in a plurality of sample barcodesdiffers from every other sample barcode in the plurality by at leastthree nucleotide positions, such as at least 3, 4, 5, 6, 7, 8, 9, 10, ormore nucleotide positions. In some embodiments, substantially degeneratesample barcodes may be known as random. In some embodiments, a samplebarcode may include a nucleic acid sequence from within a pool of knownsequences. In some embodiments, the sample barcodes may be pre-defined.In embodiments, the sample barcode includes about 1 to about 10nucleotides. In embodiments, the sample barcode includes about 3, 4, 5,6, 7, 8, 9, or about 10 nucleotides. In embodiments, the sample barcodeincludes about 3 nucleotides. In embodiments, the sample barcodeincludes about 5 nucleotides. In embodiments, the sample barcodeincludes about 7 nucleotides. In embodiments, the sample barcodeincludes about 10 nucleotides. In embodiments, the sample barcodeincludes about 6 to about 10 nucleotides.

In some embodiments, a nucleic acid comprises a label. As used herein,the term “label” or “labels” is used in accordance with their plain andordinary meanings and refer to molecules that can directly or indirectlyproduce or result in a detectable signal either by themselves or uponinteraction with another molecule. Non-limiting examples of detectablelabels include fluorescent dyes, biotin, digoxin, haptens, and epitopes.In general, a dye is a molecule, compound, or substance that can providean optically detectable signal, such as a colorimetric, luminescent,bioluminescent, chemiluminescent, phosphorescent, or fluorescent signal.In embodiments, the label is a dye. In embodiments, the dye is afluorescent dye. Non-limiting examples of dyes, some of which arecommercially available, include CF dyes (Biotium, Inc.), Alexa Fluordyes (Thermo Fisher), DyLight dyes (Thermo Fisher), Cy dyes (GEHealthscience), IRDyes (Li-Cor Biosciences, Inc.), and HiLyte dyes(Anaspec, Inc.). In embodiments, a particular nucleotide type isassociated with a particular label, such that identifying the labelidentifies the nucleotide with which it is associated. In embodiments,the label is luciferin that reacts with luciferase to produce adetectable signal in response to one or more bases being incorporatedinto an elongated complementary strand, such as in pyrosequencing. Inembodiment, a nucleotide comprises a label (such as a dye). Inembodiments, the label is not associated with any particular nucleotide,but detection of the label identifies whether one or more nucleotideshaving a known identity were added during an extension step (such as inthe case of pyrosequencing).

As used herein, the term “DNA polymerase” and “nucleic acid polymerase”are used in accordance with their plain ordinary meanings and refer toenzymes capable of synthesizing nucleic acid molecules from nucleotides(e.g., deoxyribonucleotides). Exemplary types of polymerases that may beused in the compositions and methods of the present disclosure includethe nucleic acid polymerases such as DNA polymerase, DNA- orRNA-dependent RNA polymerase, and reverse transcriptase. In some cases,the DNA polymerase is 9° N polymerase or a variant thereof, E. Coli DNApolymerase I, Bacteriophage T4 DNA polymerase, Sequenase, Taq DNApolymerase, DNA polymerase from Bacillus stearothermophilus, Bst 2.0 DNApolymerase, 9° N polymerase (exo-)A485L/Y409V, Phi29 DNA Polymerase (ϕ29DNA Polymerase), T7 DNA polymerase, DNA polymerase II, DNA polymeraseIII holoenzyme, DNA polymerase IV, DNA polymerase V, VentR DNApolymerase, Therminator™ II DNA Polymerase, Therminator™ III DNAPolymerase, or or Therminator™ IX DNA Polymerase. In embodiments, thepolymerase is a protein polymerase. Typically, a DNA polymerase addsnucleotides to the 3′-end of a DNA strand, one nucleotide at a time. Inembodiments, the DNA polymerase is a Pol I DNA polymerase, Pol II DNApolymerase, Pol III DNA polymerase, Pol IV DNA polymerase, Pol V DNApolymerase, Pol β DNA polymerase, Pol μ DNA polymerase, Pol λ, DNApolymerase, Pol σ DNA polymerase, Pol α DNA polymerase, Pol δ DNApolymerase, Pol ε DNA polymerase, Pol η DNA polymerase, Pol ι DNApolymerase, Pol κ DNA polymerase, Pol ζ DNA polymerase, Pol γ DNApolymerase, Pol θ DNA polymerase, Pol υ DNA polymerase, or athermophilic nucleic acid polymerase (e.g. Therminator γ, 9° Npolymerase (exo-), Therminator II, Therminator III, or Therminator IX).In embodiments, the DNA polymerase is a modified archaeal DNApolymerase. In embodiments, the polymerase is a reverse transcriptase.In embodiments, the polymerase is a mutant P. abyssi polymerase (e.g.,such as a mutant P. abyssi polymerase described in WO 2018/148723 or WO2020/056044).

As used herein, the term “thermophilic nucleic acid polymerase” refersto a family of DNA polymerases (e.g., 9° N™) and mutants thereof derivedfrom the DNA polymerase originally isolated from the hyperthermophilicarchaea, Thermococcus sp. 9 degrees N-7, found in hydrothermal vents atthat latitude (East Pacific Rise) (Southworth M W, et al. PNAS. 1996;93(11):5281-5285). A thermophilic nucleic acid polymerase is a member ofthe family B DNA polymerases. Site-directed mutagenesis of the 3′-5′ exomotif I (Asp-Ile-Glu or DIE) to AIA, AIE, EIE, EID or DIA yieldedpolymerase with no detectable 3′ exonuclease activity. Mutation toAsp-Ile-Asp (DID) resulted in reduction of 3′-5′ exonuclease specificactivity to <1% of wild type, while maintaining other properties of thepolymerase including its high strand displacement activity. The sequenceAIA (D141A, E143A) was chosen for reducing exonuclease. Subsequentmutagenesis of key amino acids results in an increased ability of theenzyme to incorporate dideoxynucleotides, ribonucleotides andacyclonucleotides (e.g., Therminator II enzyme from New England Biolabswith D141A/E143A/Y409V/A485L mutations); 3′-amino-dNTPs, 3′-azido-dNTPsand other 3′-modified nucleotides (e.g., NEB Therminator III DNAPolymerase with D141A/E143A/L4085/Y409A/P410V mutations, NEB TherminatorIX DNA polymerase), or γ-phosphate labeled nucleotides (e.g.,Therminator γ:D141A/E143A/W355A/L408W/R460A/Q4615/K464E/D480V/R484W/A485L). Typically,these enzymes do not have 5′-3′ exonuclease activity. Additionalinformation about thermophilic nucleic acid polymerases may be found in(Southworth M W, et al. PNAS. 1996; 93(11):5281-5285; Bergen K, et al.ChemBioChem. 2013; 14(9):1058-1062; Kumar S, et al. Scientific Reports.2012; 2:684; Fuller C W, et al. 2016; 113(19):5233-5238; Guo J, et al.Proceedings of the National Academy of Sciences of the United States ofAmerica. 2008; 105(27):9145-9150), which are incorporated herein intheir entirety for all purposes.

As used herein, the term “exonuclease activity” is used in accordancewith its ordinary meaning in the art, and refers to the removal of anucleotide from a nucleic acid by a DNA polymerase. For example, duringpolymerization, nucleotides are added to the 3′ end of the primerstrand. Occasionally a DNA polymerase incorporates an incorrectnucleotide to the 3′-OH terminus of the primer strand, wherein theincorrect nucleotide cannot form a hydrogen bond to the correspondingbase in the template strand. Such a nucleotide, added in error, isremoved from the primer as a result of the 3′ to 5′ exonuclease activityof the DNA polymerase. In embodiments, exonuclease activity may bereferred to as “proofreading.” When referring to 3′-5′ exonucleaseactivity, it is understood that the DNA polymerase facilitates ahydrolyzing reaction that breaks phosphodiester bonds at either the 3′end of a polynucleotide chain to excise the nucleotide. In embodiments,3′-5′ exonuclease activity refers to the successive removal ofnucleotides in single-stranded DNA in a 3′→5′ direction, releasingdeoxyribonucleoside 5′-monophosphates one after another. Methods forquantifying exonuclease activity are known in the art, see for exampleSouthworth et al, PNAS Vol 93, 8281-8285 (1996).

As used herein, the term “incorporating” or “chemically incorporating,”when used in reference to a primer and cognate nucleotide, refers to theprocess of joining the cognate nucleotide to the primer or extensionproduct thereof by formation of a phosphodiester bond.

As used herein, the term “selective” or “selectivity” or the like of acompound refers to the compound's ability to discriminate betweenmolecular targets. For example, a chemical reagent may selectivelymodify one nucleotide type in that it reacts with one nucleotide type(e.g., cytosines) and not other nucleotide types (e.g., adenine,thymine, or guanine). When used in the context of sequencing, such as in“selectively sequencing,” this term refers to sequencing one or moretarget polynucleotides from an original starting population ofpolynucleotides, and not sequencing non-target polynucleotides from thestarting population. Typically, selectively sequencing one or moretarget polynucleotides involves differentially manipulating the targetpolynucleotides based on known sequence. For example, targetpolynucleotides may be hybridized to a probe oligonucleotide that may belabeled (such as with a member of a binding pair) or bound to a surface.In embodiments, hybridizing a target polynucleotide to a probeoligonucleotide includes the step of displacing one strand of adouble-stranded nucleic acid. Probe-hybridized target polynucleotidesmay then be separated from non-hybridized polynucleotides, such as byremoving probe-bound polynucleotides from the starting population or bywashing away polynucleotides that are not bound to a probe. The resultis a selected subset of the starting population of polynucleotides,which is then subjected to sequencing, thereby selectively sequencingthe one or more target polynucleotides.

As used herein, the term “template polynucleotide” refers to anypolynucleotide molecule that may be bound by a polymerase and utilizedas a template for nucleic acid synthesis. A template polynucleotide maybe a target polynucleotide. In general, the term “target polynucleotide”refers to a nucleic acid molecule or polynucleotide in a startingpopulation of nucleic acid molecules having a target sequence whosepresence, amount, and/or nucleotide sequence, or changes in one or moreof these, are desired to be determined. The target sequence may be aportion of a gene, a regulatory sequence, genomic DNA, cDNA, RNAincluding mRNA, miRNA, rRNA, or others. The target sequence may be atarget sequence from a sample or a secondary target such as a product ofan amplification reaction. A target polynucleotide is not necessarilyany single molecule or sequence. For example, a target polynucleotidemay be any one of a plurality of target polynucleotides in a reaction,or all polynucleotides in a given reaction, depending on the reactionconditions. For example, in a nucleic acid amplification reaction withrandom primers, all polynucleotides in a reaction may be amplified. As afurther example, a collection of targets may be simultaneously assayedusing polynucleotide primers directed to a plurality of targets in asingle reaction. As yet another example, all or a subset ofpolynucleotides in a sample may be modified by the addition of aprimer-binding sequence (such as by the ligation of adapters containingthe primer binding sequence), rendering each modified polynucleotide atarget polynucleotide in a reaction with the corresponding primerpolynucleotide(s). In the context of selective sequencing, “targetpolynucleotide(s)” refers to the subset of polynucleotide(s) to besequenced from within a starting population of polynucleotides.

In embodiments, a target polynucleotide is a cell-free polynucleotide.In general, the terms “cell-free,” “circulating,” and “extracellular” asapplied to polynucleotides (e.g. “cell-free DNA” (cfDNA) and “cell-freeRNA” (cfRNA)) are used interchangeably to refer to polynucleotidespresent in a sample from a subject or portion thereof that can beisolated or otherwise manipulated without applying a lysis step to thesample as originally collected (e.g., as in extraction from cells orviruses). Cell-free polynucleotides are thus unencapsulated or “free”from the cells or viruses from which they originate, even before asample of the subject is collected. Cell-free polynucleotides may beproduced as a byproduct of cell death (e.g. apoptosis or necrosis) orcell shedding, releasing polynucleotides into surrounding body fluids orinto circulation. Accordingly, cell-free polynucleotides may be isolatedfrom a non-cellular fraction of blood (e.g. serum or plasma), from otherbodily fluids (e.g. urine), or from non-cellular fractions of othertypes of samples

As used herein, the terms “specific”, “specifically”, “specificity”, orthe like of a compound refers to the compound's ability to cause aparticular action, such as binding, to a particular molecular targetwith minimal or no action to other proteins in the cell.

As used herein, the terms “bind” and “bound” are used in accordance withtheir plain and ordinary meanings and refer to an association betweenatoms or molecules. The association can be direct or indirect. Forexample, bound atoms or molecules may be directly bound to one another,e.g., by a covalent bond or non-covalent bond (e.g. electrostaticinteractions (e.g. ionic bond, hydrogen bond, halogen bond), van derWaals interactions (e.g. dipole-dipole, dipole-induced dipole, Londondispersion), ring stacking (pi effects), hydrophobic interactions andthe like). As a further example, two molecules may be bound indirectlyto one another by way of direct binding to one or more intermediatemolecules, thereby forming a complex.

As used herein, the terms “sequencing”, “sequence determination”,“determining a nucleotide sequence”, and the like include determinationof a partial or complete sequence information (e.g., a sequence) of apolynucleotide being sequenced, and particularly physical processes forgenerating such sequence information. That is, the term includessequence comparisons, consensus sequence determination, contig assembly,fingerprinting, and like levels of information about a targetpolynucleotide, as well as the express identification and ordering ofnucleotides in a target polynucleotide. The term also includes thedetermination of the identification, ordering, and locations of one,two, or three of the four types of nucleotides within a targetpolynucleotide. In some embodiments, a sequencing process describedherein comprises contacting a template and an annealed primer with asuitable polymerase under conditions suitable for polymerase extensionand/or sequencing. The sequencing methods are preferably carried outwith the target polynucleotide arrayed on a solid substrate. Multipletarget polynucleotides can be immobilized on the solid support throughlinker molecules, or can be attached to particles, e.g., microspheres,which can also be attached to a solid substrate. In embodiments, thesolid substrate is in the form of a chip, a bead, a well, a capillarytube, a slide, a wafer, a filter, a fiber, a porous media, or a column.In embodiments, the solid substrate is gold, quartz, silica, plastic,glass, diamond, silver, metal, or polypropylene. In embodiments, thesolid substrate is porous.

As used herein, the terms “solid support” and “substrate” and “solidsurface” refers to discrete solid or semi-solid surfaces to which aplurality of primers may be attached. A solid support may encompass anytype of solid, porous, or hollow sphere, ball, cylinder, or othersimilar configuration composed of plastic, ceramic, metal, or polymericmaterial (e.g., hydrogel) onto which a nucleic acid may be immobilized(e.g., covalently or non-covalently). A solid support may comprise adiscrete particle that may be spherical (e.g., microspheres) or have anon-spherical or irregular shape, such as cubic, cuboid, pyramidal,cylindrical, conical, oblong, or disc-shaped, and the like. Solidsupports in the form of discrete particles may be referred to herein as“beads,” which alone does not imply or require any particular shape. Abead can be non-spherical in shape. A solid support may further comprisea polymer or hydrogel on the surface to which the primers are attached(e.g., the splint primers are covalently attached to the polymer,wherein the polymer is in direct contact with the solid support).Exemplary solid supports include, but are not limited to, glass andmodified or functionalized glass, plastics (including acrylics,polystyrene and copolymers of styrene and other materials,polypropylene, polyethylene, polybutylene, polyurethanes, Teflon™,cyclic olefin copolymers, polyimides etc.), nylon, ceramics, resins,Zeonor, silica or silica-based materials including silicon and modifiedsilicon, carbon, metals, inorganic glasses, optical fiber bundles,photopatternable dry film resists, UV-cured adhesives and polymers. Thesolid supports for some embodiments have at least one surface locatedwithin a flow cell. The solid support, or regions thereof, can besubstantially flat. The solid support can have surface features such aswells, pits, channels, ridges, raised regions, pegs, posts or the like.The term solid support is encompassing of a substrate (e.g., a flowcell) having a surface comprising a polymer coating covalently attachedthereto. In embodiments, the solid support is a flow cell. The term“flow cell” as used herein refers to a chamber including a solid surfaceacross which one or more fluid reagents can be flowed. Examples of flowcells and related fluidic systems and detection platforms that can bereadily used in the methods of the present disclosure are described, forexample, in Bentley et al., Nature 456:53-59 (2008).

As used herein, the term “sequencing reaction mixture” is used inaccordance with its plain and ordinary meaning and refers to an aqueousmixture that contains the reagents necessary to allow dNTP or dNTPanalogue to add a nucleotide to a DNA strand by a DNA polymerase. Inembodiments, the sequencing reaction mixture includes a buffer. Inembodiments, the buffer includes an acetate buffer,3-(N-morpholino)propanesulfonic acid (MOPS) buffer,N-(2-Acetamido)-2-aminoethanesulfonic acid (ACES) buffer,phosphate-buffered saline (PBS) buffer,4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffer,N-(1,1-Dimethyl-2-hydroxyethyl)-3-amino-2-hydroxypropanesulfonic acid(AMPSO) buffer, borate buffer (e.g., borate buffered saline, sodiumborate buffer, boric acid buffer), 2-Amino-2-methyl-1,3-propanediol(AMPD) buffer, N-cyclohexyl-2-hydroxyl-3-aminopropanesulfonic acid(CAPSO) buffer, 2-Amino-2-methyl-1-propanol (AMP) buffer,4-(Cyclohexylamino)-1-butanesulfonic acid (CABS) buffer, glycine-NaOHbuffer, N-Cyclohexyl-2-aminoethanesulfonic acid (CHES) buffer,tris(hydroxymethyl)aminomethane (Tris) buffer, or aN-cyclohexyl-3-aminopropanesulfonic acid (CAPS) buffer. In embodiments,the buffer is a borate buffer. In embodiments, the buffer is a CHESbuffer. In embodiments, the sequencing reaction mixture includesnucleotides, wherein the nucleotides include a reversible terminatingmoiety and a label covalently linked to the nucleotide via a cleavablelinker. In embodiments, the sequencing reaction mixture includes abuffer, DNA polymerase, detergent (e.g., Triton X), a chelator (e.g.,EDTA), and/or salts (e.g., ammonium sulfate, magnesium chloride, sodiumchloride, or potassium chloride).

As used herein, the term “sequencing cycle” is used in accordance withits plain and ordinary meaning and refers to incorporating one or morenucleotides (e.g., nucleotide analogues) to the 3′ end of apolynucleotide with a polymerase, and detecting one or more labels thatidentify the one or more nucleotides incorporated. The sequencing may beaccomplished by, for example, sequencing by synthesis, pyrosequencing,and the like. In embodiments, a sequencing cycle includes extending acomplementary polynucleotide by incorporating a first nucleotide using apolymerase, wherein the polynucleotide is hybridized to a templatenucleic acid, detecting the first nucleotide, and identifying the firstnucleotide. In embodiments, to begin a sequencing cycle, one or moredifferently labeled nucleotides and a DNA polymerase can be introduced.Following nucleotide addition, signals produced (e.g., via excitationand emission of a detectable label) can be detected to determine theidentity of the incorporated nucleotide (based on the labels on thenucleotides). Reagents can then be added to remove the 3′ reversibleterminator and to remove labels from each incorporated base. Reagents,enzymes and other substances can be removed between steps by washing.Cycles may include repeating these steps, and the sequence of eachcluster is read over the multiple repetitions.

As used herein, the term “extension” or “elongation” is used inaccordance with their plain and ordinary meanings and refer to synthesisby a polymerase of a new polynucleotide strand complementary to atemplate strand by adding free nucleotides (e.g., dNTPs) from a reactionmixture that are complementary to the template in the 5′-to-3′direction. Extension includes condensing the 5′-phosphate group of thedNTPs with the 3′-hydroxy group at the end of the nascent (elongating)DNA strand.

As used herein, the term “sequencing read” is used in accordance withits plain and ordinary meaning and refers to an inferred sequence ofnucleotide bases (or nucleotide base probabilities) corresponding to allor part of a single polynucleotide fragment. A sequencing read mayinclude 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, or morenucleotide bases. In embodiments, a sequencing read includes reading abarcode and a template nucleotide sequence. In embodiments, a sequencingread includes reading a template nucleotide sequence. In embodiments, asequencing read includes reading a barcode and not a template nucleotidesequence.

Complementary single stranded nucleic acids and/or substantiallycomplementary single stranded nucleic acids can hybridize to each otherunder hybridization conditions, thereby forming a nucleic acid that ispartially or fully double stranded. All or a portion of a nucleic acidsequence may be substantially complementary to another nucleic acidsequence, in some embodiments. As referred to herein, “substantiallycomplementary” refers to nucleotide sequences that can hybridize witheach other under suitable hybridization conditions. Hybridizationconditions can be altered to tolerate varying amounts of sequencemismatch within complementary nucleic acids that are substantiallycomplementary. Substantially complementary portions of nucleic acidsthat can hybridize to each other can be 75% or more, 76% or more, 77% ormore, 78% or more, 79% or more, 80% or more, 81% or more, 82% or more,83% or more, 84% or more, 85% or more, 86% or more, 87% or more, 88% ormore, 89% or more, 90% or more, 91% or more, 92% or more, 93% or more,94% or more, 95% or more, 96% or more, 97% or more, 98% or more or 99%or more complementary to each other. In some embodiments substantiallycomplementary portions of nucleic acids that can hybridize to each otherare 100% complementary. Nucleic acids, or portions thereof, that areconfigured to hybridize to each other often comprise nucleic acidsequences that are substantially complementary to each other.

“Hybridize” shall mean the annealing of a nucleic acid sequence toanother nucleic acid sequence (e.g., one single-stranded nucleic acid(such as a primer) to another nucleic acid) based on the well-understoodprinciple of sequence complementarity. In an embodiment the othernucleic acid is a single-stranded nucleic acid. In some embodiments, oneportion of a nucleic acid hybridizes to itself, such as in the formationof a hairpin structure. The propensity for hybridization between nucleicacids depends on the temperature and ionic strength of their milieu, thelength of the nucleic acids and the degree of complementarity. Theeffect of these parameters on hybridization is described in, forexample, Sambrook J., Fritsch E. F., Maniatis T., Molecular cloning: alaboratory manual, Cold Spring Harbor Laboratory Press, New York (1989).As used herein, hybridization of a primer, or of a DNA extensionproduct, respectively, is extendable by creation of a phosphodiesterbond with an available nucleotide or nucleotide analogue capable offorming a phosphodiester bond, therewith. For example, hybridization canbe performed at a temperature ranging from 15° C. to 95° C. In someembodiments, the hybridization is performed at a temperature of about20° C., about 25° C., about 30° C., about 35° C., about 40° C., about45° C., about 50° C., about 55° C., about 60° C., about 65° C., about70° C., about 75° C., about 80° C., about 85° C., about 90° C., or about95° C. In other embodiments, the stringency of the hybridization can befurther altered by the addition or removal of components of the bufferedsolution.

As used herein, “specifically hybridizes” refers to preferentialhybridization under hybridization conditions where two nucleic acids, orportions thereof, that are substantially complementary, hybridize toeach other and not to other nucleic acids that are not substantiallycomplementary to either of the two nucleic acid. For example, specifichybridization includes the hybridization of a primer or capture nucleicacid to a portion of a target nucleic acid (e.g., a template, or adapterportion of a template) that is substantially complementary to the primeror capture nucleic acid. In some embodiments nucleic acids, or portionsthereof, that are configured to specifically hybridize are often about80% or more, 81% or more, 82% or more, 83% or more, 84% or more, 85% ormore, 86% or more, 87% or more, 88% or more, 89% or more, 90% or more,91% or more, 92% or more, 93% or more, 94% or more, 95% or more, 96% ormore, 97% or more, 98% or more, 99% or more or 100% complementary toeach other over a contiguous portion of nucleic acid sequence. Aspecific hybridization discriminates over non-specific hybridizationinteractions (e.g., two nucleic acids that a not configured tospecifically hybridize, e.g., two nucleic acids that are 80% or less,70% or less, 60% or less or 50% or less complementary) by about 2-foldor more, often about 10-fold or more, and sometimes about 100-fold ormore, 1000-fold or more, 10,000-fold or more, 100,000-fold or more, or1,000,000-fold or more. Two nucleic acid strands that are hybridized toeach other can form a duplex which comprises a double stranded portionof nucleic acid.

A nucleic acid can be amplified by a suitable method. The term“amplified” as used herein refers to subjecting a target nucleic acid ina sample to a process that linearly or exponentially generates ampliconnucleic acids having the same or substantially the same (e.g.,substantially identical) nucleotide sequence as the target nucleic acid,or segment thereof, and/or a complement thereof. In some embodiments anamplification reaction comprises a suitable thermal stable polymerase.Thermal stable polymerases are known in the art and are stable forprolonged periods of time, at temperature greater than 80° C. whencompared to common polymerases found in most mammals. In certainembodiments the term “amplified” refers to a method that comprises apolymerase chain reaction (PCR). Conditions conducive to amplification(i.e., amplification conditions) are well known and often comprise atleast a suitable polymerase, a suitable template, a suitable primer orset of primers, suitable nucleotides (e.g., dNTPs), a suitable buffer,and application of suitable annealing, hybridization and/or extensiontimes and temperatures. In certain embodiments an amplified product(e.g., an amplicon) can contain one or more additional and/or differentnucleotides than the template sequence, or portion thereof, from whichthe amplicon was generated (e.g., a primer can contain “extra”nucleotides (such as a 5′ portion that does not hybridize to thetemplate), or one or more mismatched bases within a hybridizing portionof the primer).

As used herein, the term “rolling circle amplification (RCA)” refers toa nucleic acid amplification reaction that amplifies a circular nucleicacid template (e.g., single-stranded DNA circles) via a rolling circlemechanism. Rolling circle amplification reaction is initiated by thehybridization of a primer to a circular, often single-stranded, nucleicacid template. The nucleic acid polymerase then extends the primer thatis hybridized to the circular nucleic acid template by continuouslyprogressing around the circular nucleic acid template to replicate thesequence of the nucleic acid template over and over again (rollingcircle mechanism). The rolling circle amplification typically producesconcatemers comprising tandem repeat units of the circular nucleic acidtemplate sequence. The rolling circle amplification may be a linear RCA(LRCA), exhibiting linear amplification kinetics (e.g., RCA using asingle specific primer), or may be an exponential RCA (ERCA) exhibitingexponential amplification kinetics. Rolling circle amplification mayalso be performed using multiple primers (multiply primed rolling circleamplification or MPRCA) leading to hyper-branched concatemers. Forexample, in a double-primed RCA, one primer may be complementary, as inthe linear RCA, to the circular nucleic acid template, whereas the othermay be complementary to the tandem repeat unit nucleic acid sequences ofthe RCA product. Consequently, the double-primed RCA may proceed as achain reaction with exponential (geometric) amplification kineticsfeaturing a ramifying cascade of multiple-hybridization,primer-extension, and strand-displacement events involving both theprimers. This often generates a discrete set of concatemeric,double-stranded nucleic acid amplification products. The rolling circleamplification may be performed in-vitro under isothermal conditionsusing a suitable nucleic acid polymerase such as Phi29 DNA polymerase.RCA may be performed by using any of the DNA polymerases that are knownin the art (e.g., a Phi29 DNA polymerase, a Bst DNA polymerase, or SDpolymerase).

A nucleic acid can be amplified by a thermocycling method or by anisothermal amplification method. In some embodiments a rolling circleamplification method is used. In some embodiments amplification takesplace on a solid support (e.g., within a flow cell) where a nucleicacid, nucleic acid library or portion thereof is immobilized. In certainsequencing methods, a nucleic acid library is added to a flow cell andimmobilized by hybridization to anchors under suitable conditions. Thistype of nucleic acid amplification is often referred to as solid phaseamplification. In some embodiments of solid phase amplification, all ora portion of the amplified products are synthesized by an extensioninitiating from an immobilized primer. Solid phase amplificationreactions are analogous to standard solution phase amplifications exceptthat at least one of the amplification oligonucleotides (e.g., primers)is immobilized on a solid support.

In some embodiments solid phase amplification comprises a nucleic acidamplification reaction comprising only one species of oligonucleotideprimer immobilized to a surface or substrate. In certain embodimentssolid phase amplification comprises a plurality of different immobilizedoligonucleotide primer species. In some embodiments solid phaseamplification may comprise a nucleic acid amplification reactioncomprising one species of oligonucleotide primer immobilized on a solidsurface and a second different oligonucleotide primer species insolution. Multiple different species of immobilized or solution basedprimers can be used. Non-limiting examples of solid phase nucleic acidamplification reactions include interfacial amplification, bridge PCRamplification, emulsion PCR, WildFire amplification (e.g., US patentpublication US20130012399), the like or combinations thereof.

In certain embodiments, a nucleic acid template comprising acomplementary forward and reverse stand of a double stranded nucleicacid, a hairpin adapter on one end, and a Y adapter on the other end, isamplified by bridge PCR amplification. The bridge PCR amplificationprocess of a nucleic acid template comprising such a configuration ismechanistically distinct from a bridge amplification that takes placefor a single stranded nucleic acid template containing no internalcomplementary regions. For example, after a denaturation step in bridgePCR of a nucleic acid template comprising such a configuration,amplicons can preferentially form an intramolecular double-strandedregion as opposed to staying double-stranded at an intermolecular scale.This enables a free 3′ end at the Y-adapter end, which is available forre-priming with additional solid-phase primers.

In some embodiments, a nucleic acid, adapter, oligonucleotide probe,template and/or substrate comprises a binding motif. In some embodimentsa binding motif is one member of a binding pair where each member of thebinding pair can bind to each other specifically and with relativelyhigh affinity. For example, typical binding pairs bind to each otherwith a Kd of less than about 10 μM, 5 μM, 1 μM, 500 nM, 250 nM, 100 nM,75 nM, 50 nM, 25 nM, 15 nM, 10 nM, 5 nM, 1 nM, or less than about 0.1nM. In some embodiments a binding pair comprises at least two members(e.g., molecules) that bind non-covalently to (e.g., associate with)each other. Members of a binding pair often bind specifically to eachother. In certain embodiments, members of a binding pair bind reversiblyto each other, for example where the association of two members of abinding pair can be dissociated by a suitable method. Non-limitingexamples of a binding pair include antibody/antigen, antibody/antibody,antibody/antibody fragment, antibody/antibody receptor, antibody/proteinA, antibody/protein G, hapten/anti-hapten, biotin/avidin,biotin/streptavidin, folic acid/folate binding protein, receptor/ligand,vitamin B12/intrinsic factor, analogues thereof, derivatives thereof,binding portions thereof, the like or combinations thereof. Non-limitingexamples of a binding motif or a member of a binding pair include anantibody, antibody fragment, reduced antibody, chemically modifiedantibody, antibody receptor, Fab, Fab′, F(ab′)2, Fv fragment,single-chain Fv (scFv), diabody (Dab), synbody, TandAbs, nanobodies,BiTEs, SMIPs, DARPins, DNLs, affibodies, Duocalins, adnectins, fynomers,Kunitz Domains AlbudAbs, DARTs, DVD-IG, Covx-bodies, peptibodies,scFv-Igs, SVD-Igs, dAb-Igs, Knob-in-Holes, triomAbs, an antigen, hapten,anti-hapten, aptamer, receptor, ligand, metal ion, avidin, streptavidin,neutravidin, biotin, B12, intrinsic factor, analogues thereof,derivatives thereof, binding portions thereof, the like or combinationsthereof.

In some embodiments a nucleic acid is directly or indirectly bound(e.g., covalently or non-covalently bound) to a suitable substrate. Incertain embodiments a substrate comprises a surface (e.g., a surface ofa flow cell, a surface of a tube, a surface of a chip), for example ametal surface (e.g. steel, gold, silver, aluminum, silicon and copper).In some embodiments a substrate (e.g., a substrate surface) is coatedand/or comprises functional groups and/or inert materials. In certainembodiments a substrate comprises a bead, a chip, a capillary, a plate,a membrane, a wafer (e.g., silicon wafers), a comb, or a pin forexample. In some embodiments a substrate comprises a bead and/or ananoparticle. A substrate can be made of a suitable material,non-limiting examples of which include a plastic or a suitable polymer(e.g., polycarbonate, poly(vinyl alcohol), poly(divinylbenzene),polystyrene, polyamide, polyester, polyvinylidene difluoride (PVDF),polyethylene, polyurethane, polypropylene, and the like), borosilicate,glass, nylon, Wang resin, Merrifield resin, metal (e.g., iron, a metalalloy, sepharose, agarose, polyacrylamide, dextran, cellulose and thelike or combinations thereof. In some embodiments a substrate comprisesa magnetic material (e.g., iron, nickel, cobalt, platinum, aluminum, andthe like). In certain embodiments a substrate comprises a magnetic bead(e.g., DYNABEADS®, hematite, AMPure XP. Magnets can be used to purifyand/or capture nucleic acids bound to certain substrates (e.g.,substrates comprising a metal or magnetic material).

Provided herein are methods and compositions for analyzing a sample(e.g., sequencing nucleic acids within a sample). A sample (e.g., asample comprising nucleic acid) can be obtained from a suitable subject.A sample can be isolated or obtained directly from a subject or partthereof. In some embodiments, a sample is obtained indirectly from anindividual or medical professional. A sample can be any specimen that isisolated or obtained from a subject or part thereof. A sample can be anyspecimen that is isolated or obtained from multiple subjects.Non-limiting examples of specimens include fluid or tissue from asubject, including, without limitation, blood or a blood product (e.g.,serum, plasma, platelets, buffy coats, or the like), umbilical cordblood, chorionic villi, amniotic fluid, cerebrospinal fluid, spinalfluid, lavage fluid (e.g., lung, gastric, peritoneal, ductal, ear,arthroscopic), a biopsy sample, celocentesis sample, cells (blood cells,lymphocytes, placental cells, stem cells, bone marrow derived cells,embryo or fetal cells) or parts thereof (e.g., mitochondrial, nucleus,extracts, or the like), urine, feces, sputum, saliva, nasal mucous,prostate fluid, lavage, semen, lymphatic fluid, bile, tears, sweat,breast milk, breast fluid, the like or combinations thereof. A fluid ortissue sample from which nucleic acid is extracted may be acellular(e.g., cell-free). Non-limiting examples of tissues include organtissues (e.g., liver, kidney, lung, thymus, adrenals, skin, bladder,reproductive organs, intestine, colon, spleen, brain, the like or partsthereof), epithelial tissue, hair, hair follicles, ducts, canals, bone,eye, nose, mouth, throat, ear, nails, the like, parts thereof orcombinations thereof. A sample may comprise cells or tissues that arenormal, healthy, diseased (e.g., infected), and/or cancerous (e.g.,cancer cells). A sample obtained from a subject may comprise cells orcellular material (e.g., nucleic acids) of multiple organisms (e.g.,virus nucleic acid, fetal nucleic acid, bacterial nucleic acid, parasitenucleic acid).

In some embodiments, a sample comprises nucleic acid, or fragmentsthereof. A sample can comprise nucleic acids obtained from one or moresubjects. In some embodiments a sample comprises nucleic acid obtainedfrom a single subject. In some embodiments, a sample comprises a mixtureof nucleic acids. A mixture of nucleic acids can comprise two or morenucleic acid species having different nucleotide sequences, differentfragment lengths, different origins (e.g., genomic origins, cell ortissue origins, subject origins, the like or combinations thereof), orcombinations thereof. A sample may comprise synthetic nucleic acid.

A subject can be any living or non-living organism, including but notlimited to a human, non-human animal, plant, bacterium, fungus, virus orprotist. A subject may be any age (e.g., an embryo, a fetus, infant,child, adult). A subject can be of any sex (e.g., male, female, orcombination thereof). A subject may be pregnant. In some embodiments, asubject is a mammal. In some embodiments, a subject is a human subject.A subject can be a patient (e.g., a human patient). In some embodimentsa subject is suspected of having a genetic variation or a disease orcondition associated with a genetic variation.

Where a range of values is provided, it is understood that eachintervening value, to the tenth of the unit of the lower limit unlessthe context clearly indicates otherwise, between the upper and lowerlimit of that range, and any other stated or unstated intervening valuein, or smaller range of values within, that stated range is encompassedwithin the invention. The upper and lower limits of any such smallerrange (within a more broadly recited range) may independently beincluded in the smaller ranges, or as particular values themselves, andare also encompassed within the invention, subject to any specificallyexcluded limit in the stated range. Where the stated range includes oneor both of the limits, ranges excluding either or both of those includedlimits are also included in the invention.

The methods and kits of the present disclosure may be applied, mutatismutandis, to the sequencing of RNA, or to determining the identity of aribonucleotide.

As used herein, the term “kit” refers to any delivery system fordelivering materials. In the context of reaction assays, such deliverysystems include systems that allow for the storage, transport, ordelivery of reaction reagents (e.g., oligonucleotides, enzymes, etc. inthe appropriate containers) and/or supporting materials (e.g.,packaging, buffers, written instructions for performing a method, etc.)from one location to another. For example, kits include one or moreenclosures (e.g., boxes) containing the relevant reaction reagentsand/or supporting materials. As used herein, the term “fragmented kit”refers to a delivery system comprising two or more separate containersthat each contain a subportion of the total kit components. Thecontainers may be delivered to the intended recipient together orseparately. For example, a first container may contain an enzyme for usein an assay, while a second container contains oligonucleotides. Incontrast, a “combined kit” refers to a delivery system containing all ofthe components of a reaction assay in a single container (e.g., in asingle box housing each of the desired components). The term “kit”includes both fragmented and combined kits.

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims. All publications, patents, and patentapplications cited herein are hereby incorporated by reference in theirentirety for all purposes.

II. Methods of Amplifying and Sequencing

Provided herein is a method of sequencing both strands of a doublestranded nucleic acid. In some embodiments, a method comprisessequencing both strands of a plurality of double stranded nucleic acids.In some embodiments, a double stranded nucleic acid is a native orendogenous nucleic acid obtained from a subject or sample. In someembodiments, a double stranded nucleic acid is a sequencing libraryinsert. In some embodiments, a double stranded nucleic acid is a targetnucleic acid that one desires to obtain a sequence of. For example, insome embodiments, a double stranded nucleic acid is fragment of genomicDNA, RNA or cDNA that one desires to obtain a sequence of A doublestranded nucleic acid may be obtained from a subject and/or sample usinga suitable method. In embodiments, the double-stranded nucleic acidincludes a first DNA strand hybridized to a second DNA strand. Inembodiments, the double-stranded nucleic acid includes a DNA strandhybridized to a RNA strand.

In some embodiments, a double stranded nucleic comprises twocomplementary nucleic acid strands. In certain embodiments, a doublestranded nucleic acid comprises a first strand and a second strand whichare complementary or substantially complementary to each other. A firststrand of a double stranded nucleic acid is sometimes referred to hereinas a forward strand and a second strand of the double stranded nucleicacid is sometime referred to herein as a reverse strand. In someembodiments, a double stranded nucleic acid comprises two opposing ends.Accordingly, a double stranded nucleic acid often comprises a first endand a second end. An end of a double stranded nucleic acid may comprisea 5′-overhang, a 3′-overhang or a blunt end. In some embodiments, one orboth ends of a double stranded nucleic acid are blunt ends. In certainembodiments, one or both ends of a double stranded nucleic acid aremanipulated to include a 5′-overhang, a 3′-overhang or a blunt end usinga suitable method. In some embodiments, one or both ends of a doublestranded nucleic acid are manipulated during library preparation suchthat one or both ends of the double stranded nucleic acid are configuredfor ligation to an adapter using a suitable method. For example, one orboth ends of a double stranded nucleic acid may be digested by arestriction enzyme, polished, end-repaired, filled in, phosphorylated(e.g., by adding a 5′-phosphate), dT-tailed, dA-tailed, the like or acombination thereof.

In embodiments, the double stranded nucleic acid, alternatively referredto as a library insert or target polynucleotide, is at least 50, 100,150, 200, 250, or 300 nucleotides in length. In embodiments, the doublestranded nucleic acid, alternatively referred to as a library insert, isat least 150, 200, 250, 300, 350, or 400 nucleotides in length. Inembodiments, the double stranded nucleic acid, alternatively referred toas a library insert, is at least 450, 500, 650, 700, 750, or 800nucleotides in length. In embodiments, the double stranded nucleic acid,alternatively referred to as a library insert, is at least 850, 900,950, 1000, 1050, or 1100 nucleotides in length.

In embodiments, the double stranded nucleic acid, alternatively referredto as a library insert, is about 50, 100, 150, 200, 250, or 300nucleotides in length. In embodiments, the double stranded nucleic acid,alternatively referred to as a library insert, is about 150, 200, 250,300, 350, or 400 nucleotides in length. In embodiments, the doublestranded nucleic acid, alternatively referred to as a library insert, isabout 450, 500, 650, 700, 750, or 800 nucleotides in length. Inembodiments, the double stranded nucleic acid, alternatively referred toas a library insert, is about 850, 900, 950, 1000, 1050, or 1100nucleotides in length. In embodiments, the double stranded nucleic acid,alternatively referred to as a library insert, is about 500-1500nucleotides in length. In embodiments, the double stranded nucleic acid,alternatively referred to as a library insert, is about 750-1500nucleotides in length. In embodiments, the double stranded nucleic acid,alternatively referred to as a library insert, is about 1-2 kilobases(kb) in length. In embodiments, the double stranded nucleic acid,alternatively referred to as a library insert, is about 300, 400, 600,or 800 nucleotides in length. In embodiments, the double strandednucleic acid, alternatively referred to as a library insert, is about250 to 600 nucleotides in length.

In embodiments, the double stranded nucleic acid is about 100, 125, 150,175, or 200 nucleotides in length. In embodiments, the double strandednucleic acid is about 200, 225, 250, 275, or 300 nucleotides in length.In embodiments, the double stranded nucleic acid is less than 150nucleotides in length. In embodiments, the double stranded nucleic acidis less than 100 nucleotides in length. In embodiments, the doublestranded nucleic acid is less than 75 nucleotides in length. Inembodiments, the double stranded nucleic acid is about 150 nucleotidesin length. In embodiments, the double stranded nucleic acid is about 100nucleotides in length. In embodiments, the double stranded nucleic acidis about 75 nucleotides in length. In embodiments, the method providessequencing both strands of a double stranded nucleic acid such thatthere is overlap in the sequencing reads of the first and second strand.For example, if the double stranded nucleic acid is short (e.g., 150-200nucleotides) it is possible to sequence the first strand and acomplementary region of the second strand (e.g., in the same read).

In embodiments, the double stranded nucleic acid is greater than 150nucleotides in length. In embodiments, the double stranded nucleic acidis greater than 200 nucleotides in length. In embodiments, the doublestranded nucleic acid is greater than 250 nucleotides in length. Inembodiments, the double stranded nucleic acid is greater than 300nucleotides in length. In embodiments, the double stranded nucleic acidis greater than 500 nucleotides in length. In embodiments, the doublestranded nucleic acid is greater than 700 nucleotides in length. Inembodiments, the double stranded nucleic acid is greater than 900nucleotides in length. In embodiments, the double stranded nucleic acidis greater than 1,000 nucleotides in length (i.e., greater than 1 kb).In embodiments, the method provides sequencing both strands of a doublestranded nucleic acid such that there is no overlap in the sequencingreads of the first and second strand, rather a portion of the firststrand and portion of the second strand.

In some embodiments, a method herein comprises ligating one or moreadapters to a double stranded nucleic acid. In some embodiments, amethod herein comprises ligating one or more adapters to a plurality ofdouble stranded nucleic acids. In some embodiments, a method hereincomprises ligating a first adapter to a first end of a double strandednucleic acid, and ligating a second adapter to a second end of a doublestranded nucleic acid. In some embodiments, the first adapter and thesecond adapter are different. For example, in certain embodiments, thefirst adapter and the second adapter may comprise different nucleic acidsequences or different structures. In some embodiments, the firstadapter is a Y-adapter and the second adapter is a hairpin adapter. Insome embodiments, the first adapter is a hairpin adapter and a secondadapter is a hairpin adapter. In certain embodiments, the first adapterand the second adapter may comprise different primer binding sites,different structures, and/or different capture sequences (e.g., asequence complementary to a capture nucleic acid). In some embodiments,some, all or substantially all of the nucleic acid sequence of a firstadapter and a second adapter are the same. In some embodiments, some,all or substantially all of the nucleic acid sequence of a first adapterand a second adapter are substantially different.

In embodiments, the method comprises (a) ligating a first adapter to afirst end of the double stranded nucleic acid, and ligating a secondadapter to a second end of the double stranded nucleic acid, wherein thesecond adapter is a hairpin adapter, thereby forming a nucleic acidtemplate; (b) annealing a first primer to the nucleic acid template,wherein the first primer comprises a sequence that is complementary to aportion of the first adapter, or a complement thereof; (c) sequencing afirst portion and a second portion of the nucleic acid template byextending the first primer, thereby generating a first read comprising afirst nucleic acid sequence of at least a first portion of the doublestranded nucleic acid, and a second read comprising a nucleic acidsequence of at least a second portion of the double stranded nucleicacid. In embodiments, the method comprises (a) ligating a first adapterto a first end of the double stranded nucleic acid, and ligating asecond adapter to a second end of the double stranded nucleic acid,wherein the second adapter is a hairpin adapter, thereby forming anucleic acid template; (b) annealing a first primer to the nucleic acidtemplate, wherein the first primer comprises a sequence that iscomplementary to a portion of the first adapter, or a complementthereof; (c) sequencing a first portion of the nucleic acid template byextending the first primer, thereby generating a first read comprising afirst nucleic acid sequence of at least a first portion of the doublestranded nucleic acid; (d) annealing a second primer to the nucleic acidtemplate, wherein the second primer comprises a sequence that iscomplementary to a sequence within a loop or stem of the hairpinadapter, or a complement thereof; and (e) sequencing a second portion ofthe nucleic acid template by extending the second primer, therebygenerating a second read comprising a nucleic acid sequence of at leasta second portion of the double stranded nucleic acid. In someembodiments, the double stranded nucleic acid comprises a forward strandand a reverse strand. In embodiments, the method comprises ligating afirst adapter to a first end of the double stranded nucleic acid, andligating a second adapter to a second end of the double stranded nucleicacid, wherein the second adapter is a hairpin adapter, thereby forming anucleic acid template in solution. Following ligation, in embodimentsthe nucleic acid templates are captured with abiotinylated-oligonucleotide complementary to the loop region. Theresulting biotin-captured complexes can then be captured and purifiedvia methods of purifications based on avidin, streptavidin, orneutravidin, and amplified. For example, the captured constructs may beamplified (e.g., amplified using a polymerase chain reaction) andimmobilized on a solid support. Additional solid phase amplificationtechniques (e.g., bridge PCR amplification) may be performed to generateclusters of nucleic acids.

In some embodiments, an adapter is a Y-adapter. In some embodiments, aY-adapter comprises a first strand and a second strand where a portionof the first strand (e.g., FIG. 1A (3′-portion)) is complementary, orsubstantially complementary, to a portion (e.g., FIG. 1A (5′-portion))of the second strand. In some embodiments, a Y-adapter comprises a firststrand and a second strand where a 3′-portion of the first strand ishybridized to a 5′-portion of the second strand. In certain embodiments,the 3′-portion of the first strand that is substantially complementaryto the 5′-portion of the second strand forms a duplex comprising doublestranded nucleic acid. Accordingly, a Y-adapter often comprises a firstend comprising a duplex region comprising double stranded nucleic acid,and a second end comprising a forked region comprising a 5′-arm (FIG. 1A(5′-arm)) and a 3′-arm (FIG. 1A (3′-arm)). In some embodiments, a5′-portion of the first stand (e.g., 5′-arm) and a 3′-portion of thesecond strand (3′-arm) are not complementary. In certain embodiments,the first and second strands of a Y-adapter are not covalently attachedto each other. In some embodiments, a Y-adapter comprises (i) a firststrand having a 5′-arm and a 3′-portion, and (ii) a second strand havinga 3′-arm and a 5′-portion, wherein the 3′-portion of the first strand issubstantially complementary to the 5′-portion of the second strand, andthe 5′-arm of the first strand is not substantially complementary to the3′-arm of the second strand. In some embodiments, a Y-adapter comprisesa structure shown in any one of FIGS. 1A, 1B, 2A, and 3. In someembodiments, the first adapter includes a sample barcode sequence, amolecular identifier sequence, or both a sample barcode sequence and amolecular identifier sequence. In some embodiments, the first adapterincludes a sample barcode sequence (e.g., a 6-10 nucleotide sequence).

In embodiments, ligating includes ligating both the 3′ end and the 5′end of the duplex region of the first adapter to the double strandednucleic acid. In embodiments, ligating includes ligating either the 3′end or the 5′ end of the duplex region of the first adapter to thedouble stranded nucleic acid. In embodiments, ligating includes ligatingthe 5′ end of the duplex region of the first adapter to the doublestranded nucleic acid and not the 3′ end of the duplex region. Inembodiments, the method includes ligating a first adapter to a first endof the double stranded nucleic acid wherein both strands of the doublestranded nucleic acid are ligated to the first adapter. In embodiments,the method includes ligating a first adapter to a first end of thedouble stranded nucleic acid wherein one strand of the double strandednucleic acid is ligated to the first adapter.

In some embodiments, each strand of a Y-adapter, each of thenon-complementary arms of a Y-adapter, or a duplex portion of aY-adapter has a length independently selected from at least 5, at least10, at least 15, at least 25, and at least 40 nucleotides. In someembodiments, each strand of a Y-adapter, each of the non-complementaryarms of a Y-adapter, or a duplex portion of a Y-adapter has a length ina range independently selected from 15 to 500 nucleotides, 15-250nucleotides, 15 to 200 nucleotides, 15 to 150 nucleotides, 20 to 100nucleotides, 20 to 50 nucleotides and 10-50 nucleotides. In embodiments,one or both non-complementary arms of the Y-adapter is about or at leastabout 10, 15, 20, 25, 30, 35, 40, 45, 50, or more nucleotides in length.In embodiments, one or both non-complementary arms of the Y-adapter isabout or at least about 20 nucleotides in length. In embodiments, one orboth non-complementary arms of the Y-adapter is about or at least about30 nucleotides in length. In embodiments, one or both non-complementaryarms of the Y-adapter is about or at least about 40 nucleotides inlength. In embodiments, the duplex portion of a Y-adapter is about or atleast about 5, 10, 15, 20, 25, 30, or more nucleotides in length. Inembodiments, the duplex portion of a Y-adapter is about 5-50, 5-25, or10-15 nucleotides in length. In embodiments, the duplex portion of aY-adapter is about or at least about 10 nucleotides in length. Inembodiments, the duplex portion of a Y-adapter is about or at leastabout 15 nucleotides in length. In embodiments, the duplex portion of aY-adapter is about or at least about 12 nucleotides in length. Inembodiments, the duplex portion of a Y-adapter is about or at leastabout 20 nucleotides in length.

In some embodiments, a Y-adapter comprises a first end comprising aduplex region comprising double stranded nucleic acid, and a second endcomprising a forked region, where the first end is configured forligation to an end of double stranded nucleic acid (e.g., a nucleic acidfragment, e.g., a library insert). In embodiments, a duplex end of aY-adapter comprises a 5′-overhang or a 3′-overhang that is complementaryto a 3′-overhang or a 5′-overhang of an end of a double stranded nucleicacid. In some embodiments, a duplex end of a Y-adapter comprises a bluntend that can be ligated to a blunt end of a double stranded nucleicacid. In certain embodiment, a duplex end of a Y-adapter comprises a5′-end that is phosphorylated.

In some embodiments, the first and/or second adapter (e.g., one or bothstrands of a Y-adapter) comprise one or more of a primer binding site, acapture nucleic acid binding site (e.g., a nucleic acid sequencecomplementary to a capture nucleic acid), a UMI, a sample barcode, asequencing adapter, a label, a binding motif, the like or combinationsthereof. In some embodiments, a non-complementary portion (e.g., 5′-armand/or 3′-arm) of a Y-adapter comprises one or more of a primer bindingsite, a capture nucleic acid binding site (e.g., a nucleic acid sequencecomplementary to a capture nucleic acid), a UMI, a sample barcode, asequencing adapter, a label, a binding motif, the like or combinationsthereof. In certain embodiments, a non-complementary portion of aY-adapter comprises a primer binding site. In certain embodiments, anon-complementary portion of a Y-adapter comprises a binding site for acapture nucleic acid. In certain embodiments, a non-complementaryportion of a Y-adapter comprises a primer binding site and a UMI. Incertain embodiments, a non-complementary portion of a Y-adaptercomprises a binding motif. In embodiments, the first and/or secondadapter (e.g., one or both strands of a Y-adapter) does not comprise aUMI or sample barcode.

In certain embodiments, a complementary strand (e.g., a 3′-portion or5′-portion) of a Y-adapter comprises a primer binding site. In certainembodiments, a complementary strand (e.g., a 3′-portion or 5′-portion)of a Y-adapter comprises a binding site for a capture nucleic acid. Incertain embodiments, a complementary strand (e.g., a 3′-portion or5′-portion) of a Y-adapter comprises a primer binding site and a UMI. Incertain embodiments, a complementary strand (e.g., a 3′-portion or5′-portion) of a Y-adapter comprises a binding motif.

In some embodiments, each of the non-complementary portions (i.e., arms)of a Y-adapter independently have a predicted, calculated, mean, averageor absolute melting temperature (Tm) that is greater than 50° C.,greater than 55° C., greater than 60° C., greater than 65° C., greaterthan 70° C. or greater than 75° C. In some embodiments, each of thenon-complementary portions of a Y-adapter independently have apredicted, estimated, calculated, mean, average or absolute meltingtemperature (Tm) that is in a range of 50-100° C., 55-100° C., 60-100°C., 65-100° C., 70-100° C., 55-95° C., 65-95° C., 70-95° C., 55-90° C.,65-90° C., 70-90° C., or 60-85° C. In embodiments, the Tm is about or atleast about 70° C. In embodiments, the Tm is about or at least about 75°C. In embodiments, the Tm is about or at least about 80° C. Inembodiments, the Tm is a calculated Tm. Tm's are routinely calculated bythose skilled in the art, such as by commercial providers of customoligonucleotides. In embodiments, the Tm for a given sequence isdetermined based on that sequence as an independent oligo. Inembodiments, Tm is calculated using web-based algorithms, such asPrimer3 and Primer3Plus(www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi) usingdefault parameters. The Tm of a non-complementary portion of a Y-adaptercan be changed (e.g., increased) to a desired Tm using a suitablemethod, for example by changing (e.g., increasing) GC content, changing(e.g., increasing) length and/or by the inclusion of modifiednucleotides, nucleotide analogues and/or modified nucleotides bonds,non-limiting examples of which include locked nucleic acids (LNAs, e.g.,bicyclic nucleic acids), bridged nucleic acids (BNAs, e.g., constrainednucleic acids), CS-modified pyrimidine bases (for example, 5-methyl-dC,propynyl pyrimidines, among others) and alternate backbone chemistries,for example peptide nucleic acids (PNAs), morpholinos, the like orcombinations thereof. Accordingly, in some embodiments, each of thenon-complementary portion of a Y-adapter independently comprise one ormore modified nucleotides, nucleotide analogues and/or modifiednucleotides bonds.

In some embodiments, each of the non-complementary portions of aY-adapter independently comprise a GC content of greater than 40%,greater than 50%, greater than 55%, greater than 60% greater than 65% orgreater than 70%. In certain embodiments, each of the non-complementaryportions of a Y-adapter independently comprise a GC content in a rangeof 40-100%, 50-100%, 60-100% or 70-100%. In embodiments, one or bothnon-complementary portions of a Y-adapter have a GC content of about ormore than about 40%. In embodiments, one or both non-complementaryportions of a Y-adapter have a GC content of about or more than about50%. In embodiments, one or both non-complementary portions of aY-adapter have a GC content of about or more than about 60%. Non-basemodifiers can also be incorporated into a non-complementary portion of aY-adapter to increase Tm, non-limiting examples of which include a minorgrove binder (MGB), spermine, G-clamp, a Uaq anthraquinone cap, the likeor combinations thereof.

In certain embodiments, a duplex region of a Y-adapter comprises apredicted, estimated, calculated, mean, average or absolute Tm in arange of 30-70° C., 35-65° C., 35-60° C., 40-65° C., 40-60° C., 35-55°C., 40-55° C., 45-50° C. or 40-50° C. In embodiments, the Tm of a duplexregion of the Y-adapter is about or more than about 30° C. Inembodiments, the Tm of a duplex region of the Y-adapter is about or morethan about 35° C. In embodiments, the Tm of a duplex region of theY-adapter is about or more than about 40° C. In embodiments, the Tm of aduplex region of the Y-adapter is about or more than about 45° C. Inembodiments, the Tm of a duplex region of the Y-adapter is about or morethan about 50° C.

In some embodiments, an adapter is hairpin adapter. In some embodiments,a hairpin adapter comprises a single nucleic acid strand comprising astem-loop structure. A hairpin adapter can be any suitable length. Insome embodiments, a hairpin adapter is at least 40, at least 50, or atleast 100 nucleotides in length. In some embodiments, a hairpin adapterhas a length in a range of 45 to 500 nucleotides, 75-500 nucleotides, 45to 250 nucleotides, 60 to 250 nucleotides or 45 to 150 nucleotides. Insome embodiments, a hairpin adapter comprises a nucleic acid having a5′-end, a 5′-portion, a loop, a 3′-portion and a 3′-end (e.g., arrangedin a 5′ to 3′ orientation). In some embodiments, the 5′ portion of ahairpin adapter is annealed and/or hybridized to the 3′ portion of thehairpin adapter, thereby forming a stem portion of the hairpin adapter.In some embodiments, the 5′ portion of a hairpin adapter issubstantially complementary to the 3′ portion of the hairpin adapter. Incertain embodiments, a hairpin adapter comprises a stem portion (i.e.,stem) and a loop, wherein the stem portion is substantially doublestranded thereby forming a duplex. In some embodiments, the loop of ahairpin adapter comprises a nucleic acid strand that is notcomplementary (e.g., not substantially complementary) to itself or toany other portion of the hairpin adapter. In some embodiments, a hairpinadapter comprises a structure shown in any one of FIGS. 1, 2B, 4 and 5.In some embodiments, the second adapter includes a sample barcodesequence, a molecular identifier sequence, or both a sample barcodesequence and a molecular identifier sequence. In some embodiments, thesecond adapter includes a sample barcode sequence.

In some embodiments, a duplex region or stem portion of a hairpinadapter comprises an end that is configured for ligation to an end ofdouble stranded nucleic acid (e.g., a nucleic acid fragment, e.g., alibrary insert). In embodiments, an end of a duplex region or stemportion of a hairpin adapter comprises a 5′-overhang or a 3′-overhangthat is complementary to a 3′-overhang or a 5′-overhang of one end of adouble stranded nucleic acid. In some embodiments, an end of a duplexregion or stem portion of a hairpin adapter comprises a blunt end thatcan be ligated to a blunt end of a double stranded nucleic acid. Incertain embodiment, an end of a duplex region or stem portion of ahairpin adapter comprises a 5′-end that is phosphorylated. In someembodiments, a stem portion of a hairpin adapter is at least 15, atleast 25, or at least 40 nucleotides in length. In some embodiments, astem portion of a hairpin adapter has a length in a range of 15 to 500nucleotides, 15-250 nucleotides, 15 to 200 nucleotides, 15 to 150nucleotides, 20 to 100 nucleotides or 20 to 50 nucleotides.

In embodiments, ligating includes ligating both the 3′ end and the 5′end of the duplex region of the second adapter to the double strandednucleic acid. In embodiments, ligating includes ligating either the 3′end or the 5′ end of the duplex region of the second adapter to thedouble stranded nucleic acid. In embodiments, ligating includes ligatingthe 5′ end of the duplex region of the second adapter to the doublestranded nucleic acid and not the 3′ end of the duplex region.

In some embodiments, a loop of a hairpin adapter comprise one or more ofa primer binding site, a capture nucleic acid binding site (e.g., anucleic acid sequence complementary to a capture nucleic acid), a UMI, asample barcode, a sequencing adapter, a label, the like or combinationsthereof. In certain embodiments, a loop of a hairpin adapter comprises aprimer binding site. In certain embodiments, a loop of a hairpin adaptercomprises a primer binding site and a UMI. In certain embodiments, aloop of a hairpin adapter comprises a binding motif.

In some embodiments, a loop of a hairpin adapter has a predicted,calculated, mean, average or absolute melting temperature (Tm) that isgreater than 50° C., greater than 55° C., greater than 60° C., greaterthan 65° C., greater than 70° C. or greater than 75° C. In someembodiments, a loop of a hairpin adapter has a predicted, estimated,calculated, mean, average or absolute melting temperature (Tm) that isin a range of 50-100° C., 55-100° C., 60-100° C., 65-100° C., 70-100°C., 55-95° C., 65-95° C., 70-95° C., 55-90° C., 65-90° C., 70-90° C., or60-85° C. In embodiments, the Tm of the loop is about 65° C. Inembodiments, the Tm of the loop is about 75° C. In embodiments, the Tmof the loop is about 85° C. The Tm of a loop of a hairpin adapter can bechanged (e.g., increased) to a desired Tm using a suitable method, forexample by changing (e.g., increasing GC content), changing (e.g.,increasing) length and/or by the inclusion of modified nucleotides,nucleotide analogues and/or modified nucleotides bonds, non-limitingexamples of which include locked nucleic acids (LNAs, e.g., bicyclicnucleic acids), bridged nucleic acids (BNAs, e.g., constrained nucleicacids), CS-modified pyrimidine bases (for example, 5-methyl-dC, propynylpyrimidines, among others) and alternate backbone chemistries, forexample peptide nucleic acids (PNAs), morpholinos, the like orcombinations thereof. Accordingly, in some embodiments, a loop of ahairpin adapter comprises one or more modified nucleotides, nucleotideanalogues and/or modified nucleotides bonds.

In some embodiments, a loop of a hairpin adapter independently comprisesa GC content of greater than 40%, greater than 50%, greater than 55%,greater than 60% greater than 65% or greater than 70%. In certainembodiments, a loop of a hairpin adapter independently comprises a GCcontent in a range of 40-100%, 50-100%, 60-100% or 70-100%. Inembodiments, the loops has a GC content of about or more than about 40%.In embodiments, the loops has a GC content of about or more than about50%. In embodiments, the loops has a GC content of about or more thanabout 60%. Non-base modifiers can also be incorporated into a loop of ahairpin adapter to increase Tm, non-limiting examples of which include aminor grove binder (MGB), spermine, G-clamp, a Uaq anthraquinone cap,the like or combinations thereof. A loop of a hairpin adapter can be anysuitable length. In some embodiments, a loop of a hairpin adapter is atleast 15, at least 25, or at least 40 nucleotides in length. In someembodiments, a hairpin adapter has a length in a range of 15 to 500nucleotides, 15-250 nucleotides, 20 to 200 nucleotides, 30 to 150nucleotides or 50 to 100 nucleotides.

In certain embodiments, a duplex region or stem region of a hairpinadapter comprises a predicted, estimated, calculated, mean, average orabsolute Tm in a range of 30-70° C., 35-65° C., 35-60° C., 40-65° C.,40-60° C., 35-55° C., 40-55° C., 45-50° C. or 40-50° C. In embodiments,the Tm of the stem region is about or more than about 35° C. Inembodiments, the Tm of the stem region is about or more than about 40°C. In embodiments, the Tm of the stem region is about or more than about45° C. In embodiments, the Tm of the stem region is about or more thanabout 50° C.

In some embodiments, a method comprises ligating a first adapter to afirst end of a double stranded nucleic acid, and ligating a secondadapter to a second end of the double stranded nucleic acid, wherein thesecond adapter is a hairpin adapter, thereby forming a nucleic acidtemplate. The first adapter can be a Y-adapter or a hairpin adapter. Insome embodiments, the first adapter is a Y-adapter. Accordingly, in someembodiments, a nucleic acid template comprises a first adapter, a doublestranded nucleic acid (e.g., a library insert), and a hairpin adapter.In some embodiments, a nucleic acid template is a single strand of anucleic acid comprising single-stranded non-complementary portions andcomplementary portions that are capable of forming double-strandedregions. In certain embodiments, a nucleic acid template comprises astructure shown in FIG. 1A or 1C. For example, when the first adapter isa Y-adapter, a nucleic acid template comprises a first strand of theY-adapter, a first strand (e.g., forward strand) of a double strandednucleic acid (e.g., a library insert), a hairpin adapter, a secondstrand (e.g., reverse strand) of the double stranded nucleic acid, and asecond strand of the Y-adapter arranged in a 5′-3′ direction. Thephrases “forward strand” and “reverse strand” as used herein, whenreferring to the double stranded nucleic acid, do not imply a directionof transcription or that either of the strands comprises a codingregion, but simply indicate that the two strands are different and arecomplementary to each other.

In embodiments, a hairpin structure is formed by joining the ends of aY-adapter after ligation to a double-stranded nucleic acid. For example,in embodiments disclosed herein relating to ligation to a hairpinadapter, ligation may instead be to a Y-adapter, followed by ligation ofthe unpaired ends of the adapter to each other. For example, the twounpaired arms may be hybridized to a splint oligonucleotide that bringsthe ends of the unpaired arms in proximity, which are then ligated witha ligase.

In embodiments, the Y-adaptor portion of a Y-adaptor-ligateddouble-stranded nucleic acid is formed from cleavage in the loop of ahairpin adapter (e.g., one or more adapters as described in U.S. Pat.No. 8,883,990, which is incorporated herein by reference for allpurposes). For example, in embodiments disclosed herein relating toligation to a Y-adapter, ligation may instead be to a hairpin adapter,followed by cleavage within the loop of the hairpin adapter to releasetwo unpaired ends. In embodiments, a hairpin adapter comprises one ormore uracil nucleotide(s) in the loop, and cleavage in the loop may beaccomplished by the combined activities of Uracil DNA glycosylase (UDG)and the DNA glycosylase-lyase Endonuclease VIII, or suitable cleavageconditions known in the art. UDG cleaves the glycosidic bond between thedeoxyribose of the DNA sugar-phosphate backbone and the uracil base, andEndonuclease VIII cleaves the AP site, effectively cleaving the loop. Inembodiments, the hairpin adapter includes a recognition sequence for acompatible restriction enzyme. In embodiments, the hairpin adapterincludes one or more ribonucleotides and cleavage in the loop isaccomplished by RNase H. In embodiments, the loop of the hairpin adapterincludes a cleavable linkage that is positioned between twonon-complementary regions of the loop. In embodiments, thenon-complementary region that is 5′ of the cleavable linkage comprises aprimer binding site that is in the range of 8 to 100 nucleotides inlength. In embodiments, the first adapter is a hairpin adapter, whereinthe hairpin adapter comprises a cleavable site in the loop. Inembodiments, the first adapter is a first hairpin adapter and the secondadapter is a hairpin adapter, wherein only the first hairpin adaptercomprises a cleavable site in the loop.

In some embodiments, a method comprises sequencing a template describedherein. In some embodiments, the sequencing comprises contacting thetemplate with a suitable polymerase. In certain embodiments, thepolymerase is in an aqueous phase. In certain embodiments, thepolymerase is soluble in an aqueous solution. In some embodiments, thepolymerase is not attached to a substrate. In some embodiments, thepolymerase is attached to a substrate. In embodiments, the polymerase isa mutant polymerase capable of incorporating modified nucleotides.

In certain embodiments, a method comprises annealing a first primer to a3′-portion of a template described herein, or to a 3′-end of acomplementary sequence of a template described herein (e.g., a 3′ end ofan amplicon of a template). In certain embodiments, a method comprisesannealing a first primer to a 3′-portion of a template described herein,where the 3′-portion of the template comprises a portion of an adapter(e.g., a first adapter). In certain embodiments, a method comprisesannealing a first primer to a 3′-portion of a template described herein,where the 3′-portion of the template comprises a portion of a Y-adapter.In certain embodiments, a method comprises annealing a first primer to a3′-arm of a Y-adapter of a template described herein, where the 3′-armof the adapter comprises a primer binding site for the first primer. Incertain embodiments, a method comprises annealing a first primer to a5′-portion of a second strand of a Y-adapter of a template describedherein, where the 5′-portion of the adapter comprises a primer bindingsite for the first primer.

In embodiments where a template comprises two hairpin adapters locatedon opposing sides of a double stranded nucleic acid, a method comprisesannealing a first primer to a portion of a first adapter of a templatedescribed herein (e.g., see FIGS. 1C, 1D and 8). In certain embodiments,a method comprises annealing a first primer to a loop of a first hairpinadapter of a template described herein, where the loop of the adaptercomprises a first primer binding site for the first primer. In someembodiments, a method comprises annealing a first primer to a stem of afirst hairpin adapter of a template described herein, where the stem ofthe adapter comprises a first primer binding site for the first primer.

In certain embodiments, a method comprises sequencing a first portion ofa nucleic acid template by extending a first primer, thereby generatinga first read comprising a first nucleic acid sequence of at least afirst portion of the double stranded nucleic acid. In some embodiments,a method comprises sequencing a reverse strand (e.g., see FIG. 1A) of anucleic acid template by extending a first primer, thereby generating afirst read comprising a nucleic acid sequence of at least a portion ofthe reverse strand of a double stranded nucleic acid.

In certain embodiments, a method comprises sequencing a second portionof a nucleic acid template by extending a second primer, therebygenerating a second read comprising a second nucleic acid sequence of atleast a second portion of the double stranded nucleic acid. In someembodiments, a method comprises sequencing a forward strand (e.g., seeFIG. 1A) of a nucleic acid template by extending a second primer,thereby generating a second read comprising a nucleic acid sequence ofat least a portion of the forward strand of a double stranded nucleicacid. In some embodiments, a method comprises annealing a second primerto the nucleic acid template, wherein the second primer comprises asequence that is complementary to a primer binding sequence locatedwithin a loop of the hairpin adapter (i.e., second adapter). In certainembodiments, a second primer is annealed to a loop of the hairpinadapter (i.e., second adapter) and a second portion of the nucleic acidtemplate (e.g., the forward strand) is sequenced by extending the secondprimer, thereby generating a second read of the nucleic acid template.

In some embodiments, a method comprises (i) hybridizing a first primerto a 3′-portion of a template where the 3′ portion of the templatecomprises a portion of a Y-adapter, (ii) sequencing a portion of a firststrand of a double-stranded nucleic acid, (iii) hybridizing a secondprimer to a loop or stem of a hairpin adapter of the template, and (iv)sequencing a portion of a second strand of the double-stranded nucleicacid. In some embodiments, the methods herein can be applied to anamplicon or copy of a template (or complement thereof), as well as tothe original template.

In some embodiments, the step of sequencing a first portion of a nucleicacid template as described herein is conducted before, after and/orduring the step of sequencing a second portion of a nucleic acidtemplate as described herein. For example, in certain embodiments, asecond primer is annealed to a loop or stem region of a hairpin adapterand a first portion of a double stranded nucleic acid insert issequenced by extending the second primer, followed by annealing a firstprimer to a 3′-end of the template comprising a portion of a Y-adapter,and sequencing a second portion of the double stranded nucleic acidinsert by extending the first primer.

In certain embodiments, a method comprises generating amplicons of thenucleic acid template (e.g., the nucleic acid ligated to a first andsecond adapter, as described herein). Amplicons may be generated using asuitable amplification method. In certain embodiments, amplicons of atemplate are generated using a polymerase chain reaction or a rollingcircle amplification method, or a combination thereof. In certainembodiments, amplicons are generated using a polymerase chain reaction.In certain embodiments, amplicons are generated using a bridge PCRamplification method. In embodiments, amplicons are generated usingthermal bridge polymerase chain reaction (t-bPCR) amplification. Inembodiments, amplicons are generated using a chemical bridge polymerasechain reaction (c-bPCR) amplification. Chemical bridge polymerase chainreactions include fluidically cycling a denaturant (e.g., formamide) andmaintaining the temperature within a narrow temperature range (e.g.,+/−5° C.). In contrast, thermal bridge polymerase chain reactionsinclude thermally cycling between high temperatures (e.g., 85° C.-95°C.) and low temperatures (e.g., 60° C.-70° C.). Thermal bridgepolymerase chain reactions may also include a denaturant, typically at amuch lower concentration than traditional chemical bridge polymerasechain reactions. In embodiments, generating amplicons includes a thermalbridge polymerase chain reaction (t-bPCR) amplification. In embodiments,the plurality of cycles includes thermally cycling between (i) about 85°C. for about 15-30 sec for denaturation, and (ii) about 65° C. for about1 minute for annealing/extension of the primer. In embodiments, theplurality of cycles includes thermally cycling between (i) about 85° C.for about 15-30 sec for denaturation, and (ii) about 65° C. for about 30seconds for annealing/extension of the primer.

Provided herein in an aspect is a method of amplifying a double-strandednucleic acid template. In embodiments, the method includes (a) ligatinga first adapter to a first end of the double stranded nucleic acid, andligating a second adapter to a second end of the double stranded nucleicacid, wherein the second adapter is a hairpin adapter, thereby forming anucleic acid template; (b) annealing a first primer to the nucleic acidtemplate, wherein the first primer comprises a sequence that iscomplementary to a portion of the first adapter, or a complementthereof, and is not substantially complementary to a portion of thesecond adapter; (c) generating amplicons using a suitable amplificationmethod. In embodiments, the method provides a copy of the nucleic acidtemplate as a single-stranded molecule of DNA, and, advantageously,contains both forward and reverse strands of the originaldouble-stranded DNA molecule. In embodiments, the method furtherincludes sequencing the amplicons using a method known in the art ordescribed herein.

In embodiments, the method includes amplifying a double stranded nucleicacid including a first strand and a second strand, the method including:(a) ligating a first adapter to a first end of the double strandednucleic acid wherein the first adapter is a Y adapter including (i) afirst strand having a 5′-arm and a 3′-portion, and (ii) a second strandhaving a 5′-portion and a 3′-arm, wherein the 3′-portion of the firststrand is substantially complementary to the 5′-portion of the secondstrand, and the 5′-arm of the first strand is not substantiallycomplementary to the 3′-arm of the second strand, and ligating a secondadapter to a second end of the double stranded nucleic acid, wherein thesecond adapter is a hairpin adapter, thereby forming a nucleic acidtemplate; (b) annealing a primer to the nucleic acid template, whereinthe first primer includes a sequence that is complementary to a portionof the first adapter, or a complement thereof, and is not substantiallycomplementary to a portion of the second adapter, or a complementthereof; and (c) amplifying the nucleic acid template by extending theprimer using a strand-displacing polymerase, thereby generating anamplicon (e.g., a single-stranded amplicon) including a complement ofthe first and second strand of the double stranded nucleic acid. Inembodiments, the amplicon is a contiguous strand of DNA that containsthe first and second strand of the double-stranded nucleic acid. Inembodiments, the amplicon is a continuous strand lacking free 5′ and 3′ends. In embodiments, the amplicon is a single-stranded amplicon. Inembodiments, after step (a) the method includes amplifying the nucleicacid template to generate a plurality of nucleic acid templates using apolymerase chain reaction.

In embodiments, amplifying the nucleic acid template is on a solidsupport including a plurality of primers attached to the solid support,wherein the plurality of primers include a plurality of forward primerswith complementarity to a complement of the first strand of the Yadapter (e.g., the 5′ arm portion) and a plurality of reverse primerswith complementarity to the second strand of the Y adapter (e.g., the 3′arm portion), and the amplifying includes a plurality of cycles ofstrand denaturation, primer hybridization, and primer extension, therebygenerating a plurality of forward amplicons and a plurality of reverseamplicons.

In embodiments, the plurality of forward primers are covalently attachedto the solid support via a first linker and the reverse primers arecovalently attached to the solid support via a second linker. The linkertethering the polynucleotide strands may be any linker capable oflocalizing nucleic acids to arrays. The linkers may be the same, or thelinkers may be different. Solid-supported molecular arrays have beengenerated previously in a variety of ways, for example, the attachmentof biomolecules (e.g., proteins and nucleic acids) to a variety ofsubstrates (e.g., glass, plastics, or metals) underpins modernmicroarray and biosensor technologies employed for genotyping, geneexpression analysis and biological detection. Silica-based substratesare often employed as supports on which molecular arrays areconstructed, and functionalized silanes are commonly used to modifyglass to permit a click-chemistry enabled linker to tether thebiomolecule.

In embodiments, the method further includes removing the plurality ofreverse amplicons, annealing a primer to the amplicon (e.g., the firstamplicon), wherein the first primer includes a sequence that iscomplementary to a portion of the amplicon, or a complement thereof, andsequencing a portion of the first amplicon by extending the primer,thereby generating a sequencing read including a first nucleic acidsequence of at least a first portion of the double stranded nucleicacid. In embodiments, the method further includes removing the pluralityof forward amplicons, annealing a primer to the amplicon (e.g., thefirst amplicon), wherein the first primer includes a sequence that iscomplementary to a portion of the first amplicon, or a complementthereof, and sequencing a portion of the first amplicon by extending theprimer, thereby generating a sequencing read including a first nucleicacid sequence of at least a first portion of the double stranded nucleicacid.

In embodiments, amplifying includes incubation in a denaturant. Inembodiments, the denaturant is acetic acid, ethylene glycol,hydrochloric acid, nitric acid, formamide, guanidine, sodium salicylate,sodium hydroxide, dimethyl sulfoxide (DMSO), propylene glycol, urea, ora mixture thereof. In embodiments, the denaturant is an additive thatlowers a DNA denaturation temperature. In embodiments, the denaturant isbetaine, dimethyl sulfoxide (DMSO), ethylene glycol, formamide,glycerol, guanidine thiocyanate, 4-methylmorpholine 4-oxide (NMO), or amixture thereof. In embodiments, the denaturant is betaine, dimethylsulfoxide (DMSO), ethylene glycol, formamide, glycerol, guanidinethiocyanate, or 4-methylmorpholine 4-oxide (NMO).

In embodiments, amplifying includes a plurality of cycles of stranddenaturation, primer hybridization, and primer extension. Although eachcycle will include each of these three events (denaturation,hybridization, and extension), events within a cycle may or may not bediscrete. For example, each step may have different reagents and/orreaction conditions (e.g., temperatures). Alternatively, some steps mayproceed without a change in reaction conditions. For example, extensionmay proceed under the same conditions (e.g., same temperature) ashybridization. After extension, the conditions are changed to start anew cycle with a new denaturation step, thereby amplifying theamplicons. Primer extension products from an earlier cycle may serve astemplates for a later amplification cycle. In embodiments, the pluralityof cycles is about 5 to about 50 cycles. In embodiments, the pluralityof cycles is about 10 to about 45 cycles. In embodiments, the pluralityof cycles is about 10 to about 20 cycles. In embodiments, the pluralityof cycles is about 20 to about 30 cycles. In embodiments, the pluralityof cycles is 10 to 45 cycles. In embodiments, the plurality of cycles is10 to 20 cycles. In embodiments, the plurality of cycles is 20 to 30cycles. In embodiments, the plurality of cycles is about 10 to about 45cycles. In embodiments, the plurality of cycles is about 20 to about 30cycles.

In some embodiments, an amplification method comprises attaching anucleic acid template described herein to a substrate. In certainembodiments, attaching a nucleic acid template to a substrate comprisesannealing a capture nucleic acid to a template. In some embodiments, acapture nucleic acid anneals to a complementary sequence that is presenton an adapter portion of a template (e.g., a Y-adapter or hairpinadapter). In certain embodiments, a capture nucleic acid anneals to aprimer binding site located on a Y-adapter portion of a templatedescribed herein. A capture nucleic acid may anneal to a portion of aY-adapter on or near the 3′-end or 3′-side of a template. In someembodiments, a capture nucleic acid anneals to a 3′-arm of a Y-adapteron a template.

In embodiments, the nucleic acid template is provided in a clusteredarray. In embodiments, the clustered array includes a plurality ofamplicons localized to discrete sites on a solid support. Inembodiments, the solid support is a bead. In embodiments, the solidsupport is substantially planar. In embodiments, the solid support iscontained within a flow cell. Flow cells provide a convenient format forhousing an array of clusters produced by the methods described herein,in particular when subjected to an SBS or other detection technique thatinvolves repeated delivery of reagents in cycles. For example, toinitiate a first SBS cycle, one or more labeled nucleotides and a DNApolymerase in a buffer, can be flowed into/through a flow cell thathouses an array of clusters. The clusters of an array where primerextension causes a labeled nucleotide to be incorporated can then bedetected. Optionally, the nucleotides can further include a reversibletermination moiety that temporarily halts further primer extension oncea nucleotide has been added to a primer. For example, a nucleotideanalog having a reversible terminator moiety can be added to a primersuch that subsequent extension cannot occur until a deblocking agent(e.g., a reducing agent) is delivered to remove the moiety. Thus, forembodiments that use reversible termination, a deblocking reagent (e.g.,a reducing agent) can be delivered to the flow cell (before, during, orafter detection occurs). Washes can be carried out between the variousdelivery steps as needed. The cycle can then be repeated N times toextend the primer by N nucleotides, thereby detecting a sequence oflength N. Example SBS procedures, fluidic systems and detectionplatforms that can be readily adapted for use with an array produced bymethods of the present disclosure are described, for example, in Bentleyet al., Nature 456:53-59 (2008), US Patent Publication 2018/0274024, WO2017/205336, US Patent Publication 2018/0258472, each of which areincorporated herein in their entirety for all purposes

In some embodiments, an amplification method comprises annealing aprimer or capture nucleic acid to a portion of a Y-adapter on or near a3′-end of a template, and extending the primer using a polymerase,thereby generating a first amplicon (first copy) of the template. Incertain embodiments, a 3′-end of the first amplicon is annealed toanother primer or capture nucleic acid, which is then extended togenerate a second amplicon. The amplification process continues until aplurality of first amplicons (e.g., a set of first amplicons) and aplurality of second amplicons (e.g., a set of second amplicons) aregenerated. An exemplary bridge amplification process is shown in FIGS.6A and 6B. In embodiments, a bridge PCR amplification method produces afirst set of amplicons that are complementary to an original template,and a second set of amplicons that have nucleic acid sequencessubstantially identical to the original template, where both the firstand second sets of amplicons are attached to a substrate (e.g., asubstrate of a flow cell). After bridge amplification, in certainembodiments, the first set of amplicons, or alternatively the second setof amplicons, are removed from a surface or substrate using a suitablemethod, usually by restriction enzyme cleavage (e.g., see FIG. 7A wherethe X indicates a restriction enzyme cleavage site). Cleaving one strandmay be referred to as linearization. Suitable methods for linearizationare known, and described in more detail in U.S. Patent Publication No.2009/0118128, which is incorporated herein by reference in its entirety.For example, the first strand may be cleaved by exposing the firststrand to a mixture containing a glycosylase and one or more suitableendonucleases. In embodiments, cleaving includes chemically cleaving onestrand at a cleavable site. In embodiments, the cleavable site includesa diol linker, disulfide linker, photocleavable linker, abasic site,deoxyuracil triphosphate (dUTP), deoxy-8-Oxo-guanine triphosphate(d-8-oxoG), methylated nucleotide, ribonucleotide, or a sequencecontaining a modified or unmodified nucleotide that is specificallyrecognized by a cleaving agent.

Any suitable enzymatic, chemical, or photochemical cleavage reaction maybe used to cleave the cleavage site. The cleavage reaction may result inremoval of a part or the whole of the strand being cleaved. Suitablecleavage means include, for example, restriction enzyme digestion, inwhich case the cleavage site is an appropriate restriction site for theenzyme which directs cleavage of one or both strands of a duplextemplate; RNase digestion or chemical cleavage of a bond between adeoxyribonucleotide and a ribonucleotide, in which case the cleavagesite may include one or more ribonucleotides; chemical reduction of adisulfide linkage with a reducing agent (e.g., THPP or TCEP), in whichcase the cleavage site should include an appropriate disulfide linkage;chemical cleavage of a diol linkage with periodate, in which case thecleavage site should include a diol linkage; generation of an abasicsite and subsequent hydrolysis, etc. In embodiments, the cleavage siteis included in the surface immobilized primer (e.g., within thepolynucleotide sequence of the primer). In embodiments, one strand ofthe double-stranded amplification product (or the surface immobilizedprimer) may include a diol linkage which permits cleavage by treatmentwith periodate (e.g., sodium periodate). It will be appreciated thatmore than one diol can be included at the cleavage site. One or morediol units may be incorporated into a polynucleotide using standardmethods for automated chemical DNA synthesis. Polynucleotide primersincluding one or more diol linkers can be conveniently prepared bychemical synthesis. The diol linker is cleaved by treatment with anysubstance which promotes cleavage of the diol (e.g., a diol-cleavingagent). In embodiments, the diol-cleaving agent is periodate, e.g.,aqueous sodium periodate (NaIO4). Following treatment with thediol-cleaving agent (e.g., periodate) to cleave the diol, the cleavedproduct may be treated with a “capping agent” in order to neutralizereactive species generated in the cleavage reaction. Suitable cappingagents for this purpose include amines, e.g., ethanolamine orpropanolamine.

In another aspect is provided a method of sequencing a first portion anda second portion of a double-stranded nucleic acid, the method including(a) ligating a first adapter to a first end of the double strandednucleic acid, and ligating a second adapter to a second end of thedouble stranded nucleic acid, wherein the second adapter is a hairpinadapter, thereby forming a nucleic acid template; (b) displacing atleast a portion of one strand of the nucleic acid template by annealinga blocking primer to the nucleic acid template and extending theblocking primer to generate a blocking strand, wherein the blockingprimer comprises a sequence within a loop of the hairpin adapter, or acomplement thereof; (c) annealing a first sequencing primer to thenucleic acid template and sequencing a first portion of the nucleic acidtemplate by extending the first sequencing primer, thereby generating afirst read comprising a first nucleic acid sequence of at least a firstportion of the double stranded nucleic acid, wherein the firstsequencing primer comprises a sequence that is complementary to aportion of the first adapter; and (d) annealing a second sequencingprimer to the nucleic acid template and sequencing a second portion ofthe nucleic acid template by extending the second sequencing primer,thereby generating a second read comprising a second nucleic acidsequence of at least a second portion of the double stranded nucleicacid, wherein the second sequencing primer comprises a sequence that iscomplementary to a sequence within a loop of the hairpin adapter, or acomplement thereof. See FIGS. 18A-18B for an overview of the process. Inembodiments, the second adapter includes a cleavable site. Inembodiments, the blocking strand is removed prior to step d). Inembodiments, the extended sequencing primer from step c) is removedprior to step d). The blocking strand may remain during the firstsequencing read, and may be removed prior to starting the secondsequencing read. In embodiments, following step a) the nucleic acidtemplate is amplified. In embodiments, the method further includesamplifying the nucleic acid template. In embodiments, step c) includesannealing a second primer to the nucleic acid template, wherein thesecond primer includes a sequence that is complementary to a sequencewithin a loop of the hairpin adapter, or a complement thereof. Inembodiments, sequencing the first portion and a second portion of adouble-stranded nucleic acid is on a solid support (e.g., a polymercoated solid support). In embodiments, sequencing the first portion anda second portion of a double-stranded nucleic acid is on a solid supportincluding a plurality of primers attached to said solid support, whereinthe plurality of primers include a plurality of forward primers withcomplementarity to a complement of the first strand of the Y adapter anda plurality of reverse primers with complementarity to the second strandof the Y adapter

In embodiments, the method includes removing immobilized primers that donot contain a first or second strand of the nucleic acid template (i.e.,unused primers) on a solid support. Methods of removing immobilizedprimers can include digestion using an enzyme with exonuclease activity.Removing unused primers may serve to increase the free volume and allowfor greater accessibility. Removal of unused primers may also preventopportunities for the newly released first strand to rehybridize to anavailable surface primer, producing a priming site off the availablesurface primer, thereby facilitating the “reblocking” of the releasedfirst strand.

In embodiments, generating the blocking strand includes a plurality ofblocking primer extension cycles. In embodiments, generating theblocking strand includes extending the blocking primer by incorporatingone or more nucleotides (e.g., dNTPs) using Bst large fragment (Bst LF)polymerase, Bst2.0 polymerase, Bsu polymerase, SD polymerase, Ventexo-polymerase, Phi29 polymerase, or a mutant thereof.

After removal of one of the sets of amplicons from the substrate, theother remaining set of substrate-attached amplicons is subjected tosequencing by annealing a first sequencing primer at the 3′-end(3′-region) of each of the amplicons (formerly a portion of theY-adapter), and extending the first primer to obtain a sequence read ofa 3′ portion of each of the amplicons, which comprises a sequence of afirst strand of the original double stranded insert. Before, during orafter obtaining a sequence read of the 3′-portion of the amplicons, asecond primer is annealed to the loop of each of the set of amplicons(i.e., the loop portion of the hairpin adapter used to make thetemplate) and the second primer is used to obtain a second sequence readof a second portion of the amplicon, which comprises a sequence of theopposite strand of the original doubled stranded insert. The processdescribed above obtains a sequence read of both strands of the originaldouble stranded nucleic acid insert from a single set of substantiallyidentical amplicons. In some embodiments, sequencing method is completeat this stage and does not require another amplification step.Traditional methods of paired-end sequencing that utilize bridgeamplification require a first amplification to obtain a first read ofone strand of an insert followed by a second amplification to obtain asecond read of the other strand of an insert. The required secondamplification step of traditional method introduces a substantial amountof error in the sequencing reads obtained after the secondamplification. The methods described herein, in certain embodiments, donot require a second amplification step and therefore provide for lesserror in the sequence reads obtained. Accordingly, in some embodiments,a method of sequencing both strands of a double stranded nucleic acid,as described herein, comprises, or consists essentially of, generating afirst read and a second read from the same template. In someembodiments, a method of sequencing both strands of a double strandednucleic acid, as described herein, comprises, or consists essentiallyof, generating a first read and a second read from a set of ampliconsthat are substantially complementary to a nucleic acid template. In someembodiments, a method of sequencing both strands of a double strandednucleic acid, as described herein, comprises, or consists essentiallyof, generating a first read and a second read from a set of ampliconsthat are substantially identical to a nucleic acid template.

In certain embodiments, a sequencing method provided herein comprisessequencing both strands of a double stranded nucleic acid with an errorrate of 5×10⁻⁵ or less, 1×10⁻⁵ or less, 5×10⁻⁶ or less, 1×10⁻⁶ or less,5×10⁻⁷ or less, 1×10⁻⁷ or less, 5×10⁻⁸ or less, or 1×10⁻⁸ or less. Incertain embodiments, a sequencing method provided herein comprisessequencing both strands of a double stranded nucleic acid with an errorrate of 5×10⁻⁵ to 1×10⁻⁸, 1×10⁻⁵ to 1×10⁻⁸, 5×10⁻⁵ to 1×10⁻⁷, 1×10⁻⁵ to1×10⁻⁷, 5×10⁻⁶ to 1×10⁻⁸, or 1×10⁻⁶ to 1×10⁻⁸. In certain embodiments, asequencing method provided herein comprises sequencing both strands of adouble stranded nucleic acid with an error rate of or 1×10⁻⁶ to 1×10⁻⁸.In certain embodiments, a sequencing method provided herein comprisessequencing both strands of a double stranded nucleic acid with an errorrate of 1×10⁻⁴ to 1×10⁻⁶. In certain embodiments, a sequencing methodprovided herein comprises sequencing both strands of a double strandednucleic acid with an error rate of 1×10⁻³ or less. In embodiments, asequencing method provided herein comprises sequencing both strands of adouble stranded nucleic acid with an error rate of 1×10⁻⁴ or less. Inembodiments, a sequencing method provided herein comprises sequencingboth strands of a double stranded nucleic acid with an error rate of1×10⁻⁵ or less. In embodiments, a sequencing method provided hereincomprises sequencing both strands of a double stranded nucleic acid withan error rate of 1×10⁻⁶ or less. In embodiments, a sequencing methodprovided herein comprises sequencing both strands of a double strandednucleic acid with an error rate of 1×10⁻⁷ or less. In embodiments, asequencing method provided herein comprises sequencing both strands of adouble stranded nucleic acid with an error rate of 1×10⁻⁸ or less.

Optionally, after obtaining sequences of both the first strand andsecond strand of the original double stranded insert from a single setof substantially identical amplicons (e.g., the first set of amplicons)attached to the substrate, a copy of each of the amplicons is generatedby a process comprising annealing the free 3′-end of each amplicon to asurface-bound capture nucleic acid, extending the capture nucleic acidwith a polymerase to generate third set of amplicons, removing the firstset of amplicons from the substrate, and sequencing the third set ofamplicons. In certain embodiments, the novel methods provided herein donot require this second amplification step which introduces additionalerror into the sequence reads obtained from the third set of amplicons.

In certain embodiments, templates or amplicons described herein areattached to addressable locations on a substrate using a suitable methodknown in the art or described herein.

In embodiments where a template is generated using two hairpin adapters,a template can be amplified using a rolling circle amplification method(e.g., see FIG. 8 for an overview of an embodiment of a seeding andamplification process). In such embodiments, a template can be capturedto a substrate and/or amplified using one or more capture nucleic acidsthat anneal to a loop region of one of the hairpin adapters. Capturedtemplates or amplicons can be further sequenced by a method describedherein.

In some embodiments, methods provided herein comprise sequencing atemplate nucleic acid or amplicon described herein. The methods oftemplate preparation and nucleic acid sequencing described herein can beincorporated into a suitable sequencing technique, non-limiting examplesof which include SMRT (single-molecule real-time sequencing), ionsemiconductor, pyrosequencing, sequencing by synthesis, combinatorialprobe anchor synthesis, and SOLiD sequencing (sequencing by ligation).Non-limiting sequencing platforms include those provided by Illumina®(e.g., the MiniSeq™, MiSeq™, NextSeq™, and/or NovaSeq™ sequencingsystems); Ion Torrent™ (e.g., the Ion PGM™, Ion S5™, and/or Ion Proton™sequencing systems); Pacific Biosciences (e.g., the PACBIO RS II and/orSequel II System sequencing system); ThermoFisher (e.g., a SOLID®sequencing system); or BGI Genomics (e.g., DNBSeq™ sequencing systems).See, for example U.S. Pat. Nos. 7,211,390; 7,244,559; 7,264,929;6,255,475; 6,013,445; 8,882,980; 6,664,079; and 9,416,409. In someembodiments, a sequencing method described herein does not comprise theuse of SMRT sequencing or single-molecule sequencing.

In embodiments, the method includes sequencing the first and the secondstrand of a double-stranded template and/or amplification product byextending a sequencing primer hybridized thereto. A variety ofsequencing methodologies can be used such as sequencing-by-synthesis(SBS), pyrosequencing, sequencing by ligation (SBL), or sequencing byhybridization (SBH). Pyrosequencing detects the release of inorganicpyrophosphate (PPi) as particular nucleotides are incorporated into anascent nucleic acid strand (Ronaghi, et al., Analytical Biochemistry242(1), 84-9 (1996); Ronaghi, Genome Res. 11(1), 3-11 (2001); Ronaghi etal. Science 281(5375), 363 (1998); U.S. Pat. Nos. 6,210,891; 6,258,568;and. 6,274,320, each of which is incorporated herein by reference in itsentirety). In pyrosequencing, released PPi can be detected by beingconverted to adenosine triphosphate (ATP) by ATP sulfurylase, and thelevel of ATP generated can be detected via light produced by luciferase.In this manner, the sequencing reaction can be monitored via aluminescence detection system. In both SBL and SBH methods, targetnucleic acids, and amplicons thereof, that are present at features of anarray are subjected to repeated cycles of oligonucleotide delivery anddetection. SBL methods, include those described in Shendure et al.Science 309:1728-1732 (2005); U.S. Pat. Nos. 5,599,675; and 5,750,341,each of which is incorporated herein by reference in its entirety; andthe SBH methodologies are as described in Bains et al., Journal ofTheoretical Biology 135(3), 303-7 (1988); Drmanac et al., NatureBiotechnology 16, 54-58 (1998); Fodor et al., Science 251(4995), 767-773(1995); and WO 1989/10977, each of which is incorporated herein byreference in its entirety.

In SBS, extension of a nucleic acid primer along a nucleic acid templateis monitored to determine the sequence of nucleotides in the template.The underlying chemical process can be catalyzed by a polymerase,wherein fluorescently labeled nucleotides are added to a primer (therebyextending the primer) in a template dependent fashion such thatdetection of the order and type of nucleotides added to the primer canbe used to determine the sequence of the template. A plurality ofdifferent nucleic acid fragments that have been attached at differentlocations of an array can be subjected to an SBS technique underconditions where events occurring for different templates can bedistinguished due to their location in the array. In embodiments, thesequencing step includes annealing and extending a sequencing primer toincorporate a detectable label that indicates the identity of anucleotide in the target polynucleotide, detecting the detectable label,and repeating the extending and detecting steps. In embodiments, themethods include sequencing one or more bases of a target nucleic acid byextending a sequencing primer hybridized to a target nucleic acid (e.g.,an amplification product produced by the amplification methods describedherein). In embodiments, the sequencing step may be accomplished by asequencing-by-synthesis (SBS) process. In embodiments, sequencingcomprises a sequencing by synthesis process, where individualnucleotides are identified iteratively, as they are polymerized to forma growing complementary strand. In embodiments, nucleotides added to agrowing complementary strand include both a label and a reversible chainterminator that prevents further extension, such that the nucleotide maybe identified by the label before removing the terminator to add andidentify a further nucleotide. Such reversible chain terminators includeremovable 3′ blocking groups, for example as described in U.S. Pat. No.10,738,072 and Chen et al, Proteomics & Bioinformatics, V. 11, Issue 1,2013, Pages 34-40, each of which are incorporated herein by reference.Once such a modified nucleotide has been incorporated into the growingpolynucleotide chain complementary to the region of the template beingsequenced, there is no free 3′-OH group available to direct furthersequence extension and therefore the polymerase cannot add furthernucleotides. Once the identity of the base incorporated into the growingchain has been determined, the 3′ block may be removed to allow additionof the next successive nucleotide. By ordering the products derivedusing these modified nucleotides it is possible to deduce the DNAsequence of the DNA template. Non-limiting examples of suitable labelsare described in U.S. Pat. Nos. 8,178,360, 5,188,934(4,7-dichlorofluorscein dyes); U.S. Pat. No. 5,366,860 (spectrallyresolvable rhodamine dyes); U.S. Pat. No. 5,847,162(4,7-dichlororhodamine dyes); U.S. Pat. No. 4,318,846 (ether-substitutedfluorescein dyes); U.S. Pat. No. 5,800,996 (energy transfer dyes); U.S.Pat. No. 5,066,580 (xanthene dyes): U.S. Pat. No. 5,688,648 (energytransfer dyes); and the like.

Sequencing includes, for example, detecting a sequence of signals.Examples of sequencing include, but are not limited to, sequencing bysynthesis (SBS) processes in which reversibly terminated nucleotidescarrying fluorescent dyes are incorporated into a growing strand,complementary to the target strand being sequenced. In embodiments, thenucleotides are labeled with up to four unique fluorescent dyes. Inembodiments, the nucleotides are labeled with at least two uniquefluorescent dyes. In embodiments, the readout is accomplished byepifluorescence imaging. A variety of sequencing chemistries areavailable, non-limiting examples of which are described herein.

III. Methods of Selectively Capturing and Methods of SelectivelySequencing

In an aspect is provided a method of selectively capturing adouble-stranded nucleic acid. In embodiments, the method comprises (a)ligating a first adapter to a first end of the double-stranded nucleicacid, and ligating a second adapter to a second end of thedouble-stranded nucleic acid, wherein the second adapter is a hairpinadapter; (b) displacing at least a portion of one strand of thedouble-stranded nucleic acid from step (a); (c) hybridizing a probeoligonucleotide to the displaced portion of the double-stranded nucleicacid; (d) separating the probe-hybridized double-stranded nucleic acidfrom nucleic acids not hybridized to a probe. In embodiments, the methodfurther includes amplifying double-stranded nucleic acid of step (d).The double-stranded nucleic acid of step (d) may be amplified by asuitable method to generate amplicons. For example, amplicons may begenerated in solution. In some embodiments, amplifying includes solidphase nucleic acid amplification. In embodiments, the method ofgenerating amplicons of the nucleic acid template includes a polymerasechain reaction. In embodiments, the polymerase chain reaction includes abridge PCR or isothermal amplification method. In embodiments, themethod further includes sequencing the amplicons.

In an aspect is provided a method of preparing a double-stranded nucleicacid for capture and/or sequencing. In embodiments, the method comprises(a) ligating a first adapter to a first end of the double-strandednucleic acid, and ligating a second adapter to a second end of thedouble-stranded nucleic acid, wherein the second adapter is a hairpinadapter; (b) hybridizing a probe oligonucleotide to a loop of thehairpin adapter; and (c) extending the probe oligonucleotide with apolymerase.

In an aspect is provided a method of selectively capturing and enrichinga region of a double-stranded nucleic acid. In embodiments, the methodcomprises (a) ligating a first adapter to a first end of thedouble-stranded nucleic acid, and ligating a second adapter to a secondend of the double-stranded nucleic acid, wherein the second adapter is ahairpin adapter; (b) hybridizing a probe oligonucleotide to a loop ofthe hairpin adapter; (c) separating the probe-hybridized double-strandednucleic acid from nucleic acids not hybridized to a probe; (d)amplifying probe-hybridized double-stranded nucleic acid of step (c) togenerate double-stranded amplification products. In embodiments, themethod further includes immobilizing the double-stranded amplificationproducts on a solid support. In embodiments, the method includesproviding a solid support including a plurality of immobilizedoligonucleotide primers attached to the solid support via a linker,wherein the plurality of oligonucleotide primers include a plurality offorward primers and a plurality of reverse primers, amplifying thedouble-stranded amplification products of step (d) by using theoligonucleotide primers attached to the solid support to generate aplurality of double-stranded amplification products. In embodiments,generating a double-stranded amplification product includes bridgepolymerase chain reaction (bPCR) amplification, solid-phase rollingcircle amplification (RCA), solid-phase exponential rolling circleamplification (eRCA), solid-phase recombinase polymerase amplification(RPA), solid-phase helicase dependent amplification (HDA), templatewalking amplification, or emulsion PCR on particles, or combinations ofthe methods. In embodiments, generating a double-stranded amplificationproduct includes a bridge polymerase chain reaction amplification. Inembodiments, generating a double-stranded amplification product includesa thermal bridge polymerase chain reaction (t-bPCR) amplification. Inembodiments, generating a double-stranded amplification product includesa chemical bridge polymerase chain reaction (c-bPCR) amplification.Chemical bridge polymerase chain reactions include fluidically cycling adenaturant (e.g., formamide) and maintaining the temperature within anarrow temperature range (e.g., +/−5° C.). In contrast, thermal bridgepolymerase chain reactions include thermally cycling between hightemperatures (e.g., 85° C.-95° C.) and low temperatures (e.g., 60°C.-70° C.). Thermal bridge polymerase chain reactions may also include adenaturant, typically at a much lower concentration than traditionalchemical bridge polymerase chain reactions.

In embodiments, generating a double-stranded amplification productincludes amplifying the template polynucleotide or complement thereof ona solid support including a plurality of primers attached to the solidsupport, wherein the plurality of primers include a plurality of forwardprimers with complementarity to the template polynucleotide and aplurality of reverse primers with complementarity to a complement of thetemplate polynucleotide, and the amplifying includes a plurality ofcycles of strand denaturation, primer hybridization, and primerextension.

In an aspect is provided a method of selectively capturing and enrichinga region of a double-stranded nucleic acid. In embodiments, the methodcomprises (a) ligating a first adapter to a first end of thedouble-stranded nucleic acid, and ligating a second adapter to a secondend of the double-stranded nucleic acid, wherein the second adapter is ahairpin adapter; (b) displacing at least a portion of one strand of thedouble-stranded nucleic acid from step (a); (c) hybridizing a probeoligonucleotide to the displaced portion of the double-stranded nucleicacid; (d) extending the probe oligonucleotide with a polymerase. Inembodiments, the probe oligonucleotide acts as a primer. In embodiments,both the first and second adapter are hairpin adapters and extending theprimer with a polymerase includes rolling circle amplification (RCA)(see, e.g., Lizardi et al., Nat. Genet. 19:225-232 (1998), which isincorporated herein by reference in its entirety). Several suitable RCAmethods are known in the art. For example, RCA amplifies circular DNA bypolymerase extension of an amplification primer complementary to aportion of the template polynucleotide. This process generates copies ofthe circular DNA template such that multiple copies of a DNA sequencearranged end to end in tandem are generated (i.e., a concatemer). Inembodiments, extending the primer with a polymerase includes exponentialrolling circle amplification (eRCA). Exponential RCA is similar to thelinear process except that it uses a second primer of identical sequenceto the DNA circle (Lizardi et al. Nat. Genet. 19:225 (1998)). Thistwo-primer system achieves isothermal, exponential amplification.Exponential RCA has been applied to the amplification of non-circularDNA through the use of a linear probe that binds at both of its ends tocontiguous regions of a target DNA followed by circularization using DNAligase (Nilsson et al. Science 265(5181):208 5(1994)). In embodiments,the probe oligonucleotide hybridizes within a loop of the first hairpinadapter. In embodiments, the probe oligonucleotide hybridizes within aloop of the second hairpin adapter.

In embodiments, the probe oligonucleotide contains a sequence capable ofhybridizing to a mutated sequence (i.e., a hotspot sequence) asidentified in Catalogue of Somatic Mutations In Cancer (COSMIC),full-length genes, copy number genes, single nucleotide polymorphisms(SNPs), or inter- and intragenic gene fusions. In embodiments, the probeoligonucleotide contains a sequence capable of hybridizing to a regionof interest, such as a gene associated with cancer (e.g., lung, colon,breast, ovarian, melanoma, or prostate cancer) see for example Simen BB, Arch Pathol Lab Med; 139(4):508-517 (2015) or Singh R R, J Mol Diagn.September; 15(5):607-22 (2013); a gene associated with a disease (e.g.,retinopathy, epilepsy, immunodeficiency, cardiomyopathy, hearing loss,muscular dystrophy, aneuploidy), see for example S. Yohe et al. Vol.139, No. 2, pp. 204-210 (2015) or Rehm H L. Nat Rev Genet. 14(4):295-300(2013); or a gene associated with persisting pain (see for exampleKringel et al. Front. Pharmacol. V9 Art. 1008 2018).

In embodiments, the probe oligonucleotide includes a sequence capable ofhybridizing to an oncogene and/or tumor suppressor gene sequence, or aportion thereof. Non-limiting examples of oncogenes and tumor suppressorgenes include the ABL1 gene, AKT1 gene, ALK gene, APC gene, ATM gene,BRAF gene, BRCA gene, CDH1 gene, CDKN2A gene, CSF1R gene, CTNNB1 gene,EGFR gene, ERBB2 gene, ERBB4 gene, EZH2 gene, FBXW7 gene, FGFR1 gene,FGFR2 gene, FGFR3 gene, FLT3 gene, GNA11 gene, GNAQ gene, GNAS gene,HNF1A gene, HRAS gene, IDH1 gene, IDH2 gene, JAK2 gene, JAK3 gene, KDRgene, KIT gene, KRAS gene, MET gene, MLH1 gene, MPL gene, NOTCH1 gene,NPM1 gene, NRAS gene, PDGFRA gene, PIK3CA gene, PTEN gene, PTPN11 gene,RB1 gene, RET gene, SMAD4 gene, SMARCB1 gene, SMO gene, SRC gene, STK11gene, TP53 gene, VHL gene, or a portion thereof.

In embodiments, the method comprises (a) ligating a first adapter to afirst end of the double-stranded nucleic acid, and ligating a secondadapter to a second end of the double-stranded nucleic acid, wherein thesecond adapter is a hairpin adapter; (b) displacing at least a portionof one strand of the double-stranded nucleic acid from step (a); (c)hybridizing a probe oligonucleotide to the displaced portion of thedouble-stranded nucleic acid; (d) separating the probe-hybridizeddouble-stranded nucleic acid from nucleic acids not hybridized to aprobe; and (e) sequencing the probe-hybridized double-stranded nucleicacid of step (d).

In some embodiments, a double stranded nucleic comprises twocomplementary nucleic acid strands. In certain embodiments, a doublestranded nucleic acid comprises a first strand and a second strand whichare complementary or substantially complementary to each other. A firststrand of a double stranded nucleic acid is sometimes referred to hereinas a forward strand and a second strand of the double stranded nucleicacid is sometime referred to herein as a reverse strand. In someembodiments, a double stranded nucleic acid comprises two opposing ends.Accordingly, a double stranded nucleic acid often comprises a first endand a second end. An end of a double stranded nucleic acid may comprisea 5′-overhang, a 3′-overhang or a blunt end. In some embodiments, one orboth ends of a double stranded nucleic acid are blunt ends. In certainembodiments, one or both ends of a double stranded nucleic acid aremanipulated to include a 5′-overhang, a 3′-overhang or a blunt end usinga suitable method. In some embodiments, one or both ends of a doublestranded nucleic acid are manipulated during library preparation suchthat one or both ends of the double stranded nucleic acid are configuredfor ligation to an adapter using a suitable method. For example, one orboth ends of a double stranded nucleic acid may be digested by arestriction enzyme, polished, end-repaired, filled in, phosphorylated(e.g., by adding a 5′-phosphate), dT-tailed, dA-tailed, the like or acombination thereof.

In some embodiments, a method herein comprises ligating one or moreadapters to a double stranded nucleic acid. In some embodiments, amethod herein comprises ligating one or more adapters to a plurality ofdouble stranded nucleic acids. In some embodiments, a method hereincomprises ligating a first adapter to a first end of a double strandednucleic acid, and ligating a second adapter to a second end of a doublestranded nucleic acid. In some embodiments, the first adapter and thesecond adapter are different. For example, in certain embodiments, thefirst adapter and the second adapter may comprise different nucleic acidsequences or different structures. In some embodiments, the firstadapter is a Y-adapter and the second adapter is a hairpin adapter. Insome embodiments, the first adapter is a hairpin adapter and a secondadapter is a hairpin adapter. In certain embodiments, the first adapterand the second adapter may comprise different primer binding sites,different structures, and/or different capture sequences (e.g., asequence complementary to a capture nucleic acid). In some embodiments,some, all or substantially all of the nucleic acid sequence of a firstadapter and a second adapter are the same. In some embodiments, some,all or substantially all of the nucleic acid sequence of a first adapterand a second adapter are substantially different.

In embodiments, the first adapter is a first adapter as described withrespect to other aspects disclosed herein, including with respect tomethods of sequencing described above (such as a Y-adapter or a hairpinadapter described above).

In embodiments, the second adapter is a second adapter as described withrespect to other aspects disclosed herein, including with respect tomethods of sequencing described above (such as a hairpin adapterdescribed above).

In embodiments, a hairpin structure is formed by joining the ends of aY-adapter after ligation to a double-stranded nucleic acid. For example,in embodiments disclosed herein relating to ligation to a hairpinadapter, ligation may instead be to a Y-adapter, followed by ligation ofthe unpaired ends of the adapter to each other. For example, the twounpaired arms may be hybridized to a splint oligonucleotide that bringsthe ends of the unpaired arms in proximity, which are then ligated witha ligase.

In embodiments, the Y-adaptor portion of a Y-adaptor-ligateddouble-stranded nucleic acid is formed from cleavage in the loop of ahairpin adapter. For example, in embodiments disclosed herein relatingto ligation to a Y-adapter, ligation may instead be to a hairpinadapter, followed by cleavage within the loop of the hairpin adapter torelease two unpaired ends. In embodiments, a hairpin adapter comprisesone or more uracil nucleotide(s) in the loop, and cleavage in the loopmay be accomplished by the combined activities of Uracil DNA glycosylase(UDG) and the DNA glycosylase-lyase Endonuclease VIII. UDG cleaves theglycosidic bond between the deoxyribose of the DNA sugar-phosphatebackbone and the uracil base, and Endonuclease VIII cleaves the AP site,effectively cleaving the loop. In embodiments, the hairpin adapterincludes a recognition sequence for a compatible restriction enzyme. Inembodiments, the hairpin adapter includes one or more ribonucleotidesand cleavage in the loop is accomplished by RNase H.

In embodiments, the first adapter is a Y-adapter, and the displacing atleast a portion of one strand of the double-stranded nucleic acidcomprises: (i) hybridizing a primer to a single-stranded portion of theY-adapter, and (ii) in a primer extension reaction, extending the primerwith a strand-displacing polymerase that terminates extension within aloop of the hairpin adapter at a terminating nucleotide.

In embodiments, the first adapter is a hairpin adapter, and thedisplacing at least a portion of one strand of the double-strandednucleic acid comprises: (i) hybridizing a primer within a loop of thefirst hairpin adapter, and (ii) in a primer extension reaction,extending the primer with a strand-displacing polymerase that terminatesextension within a loop of the second hairpin adapter at a terminatingnucleotide.

In embodiments, the terminating nucleotide comprises a removable groupthat blocks progression of the strand-displacing polymerase, and furtherwherein the terminating nucleotide is treated to release the removablegroup prior to sequencing. Any of a variety of suitable modificationscapable of terminating strand extensions may be used. In general, theterminating nucleotide is the nucleotide position that is modified toinhibit strand extension. The terminating nucleotide may or may not be anucleotide analogue. Thus, a terminating nucleotide is not necessarilychemically modified. For example, a terminating nucleotide may be anaturally occurring nucleotide, but is bound by another factor thatinhibits strand extension (such as a sequence-specific binding protein).Any of a variety of suitable chemical modifications and blocking groupsmay be used. In embodiments, the terminating nucleotide is a nucleotideanalog. Non-limiting examples include C3′-modifications,C2′-modifications, and phosphorodithioates.

In embodiments, the removable group is a polymer or a protein joined tothe terminating nucleotide by a cleavable linker. In embodiments, theremovable group is a polymer, such as a dendrimer. Non-limiting examplesof polymers include PEG, polyethyleneimine, and poly(amidoamide). Inembodiments, the protein is a bovine serum albumin (BSA).

In embodiments, the removable group is a protein that is non-covalentlycomplexed to the terminating nucleotide, and further wherein releasingthe protein comprises a change in reaction conditions to disrupt thecomplex. The nature of the change in reaction conditions will depend onthe nature of the protein complexed to the terminating nucleotide. Inembodiments, the change in reaction conditions includes a change intemperature. In embodiments, the change in reaction conditions includesa change in buffer conditions, such as an increase in saltconcentration. In embodiments, the change in reactions conditionsincludes the addition of another agent that competes with, inhibits, ordegrades the protein.

In embodiments, the protein is a first member of a binding paircomplexed with a second member of the binding pair that is linked to theterminating nucleotide. In embodiments, the protein is a single-strandedbinding protein that recognizes a sequence within the loop of thehairpin adapter. In embodiments, the binding pair is a binding pair asdescribed with respect to other aspects disclosed herein, including withrespect to methods of sequencing described above.

In embodiments, the terminating nucleotide is a first nucleotide analogthat base pairs with a second nucleotide analog, and the secondnucleotide analog is not present in the primer extension reaction, suchthat primer extension terminates.

In embodiments, the terminating nucleotide is an RNA nucleotide.

In embodiments, the first adapter is a Y-adapter, and the displacing atleast a portion of one strand of the double-stranded nucleic acidcomprises: (i) hybridizing a primer within a loop of the hairpinadapter, and (ii) in a primer extension reaction, extending the primerwith a strand-displacing polymerase to generate a blocking strand. Withthe formation of a double-stranded product, that is, wherein one strandis hybridized to a blocking strand, the other strand is single strandedand available for capture (e.g., hybridizing to a surface-boundcomplementary oligonucleotide) and/or sequencing. For example, see FIG.18 for an overview of an illustrative process.

In embodiments, generating the blocking strand includes extending theinvasion primer by incorporating one or more nucleotides (e.g., dNTPs)using Bst large fragment (Bst LF) polymerase, Bst2.0 polymerase, Bsupolymerase, SD polymerase, Vent exo-polymerase, Phi29 polymerase, or amutant thereof. In embodiments, the primer is about 10 to 100nucleotides in length. In embodiments, the primer is about 15 to about75 nucleotides in length. In embodiments, the primer is about 25 toabout 75 nucleotides in length. In embodiments, the primer is about 15to about 50 nucleotides in length. In embodiments, the primer is about10 to about 20 nucleotides in length.

In embodiments, the reaction conditions for the extension cycles includeincubation in a denaturant. In embodiments, the denaturant is a bufferedsolution including betaine, dimethyl sulfoxide (DMSO), ethylene glycol,formamide, glycerol, guanidine thiocyanate, 4-methylmorpholine 4-oxide(NMO), or a mixture thereof. In embodiments, the denaturant is abuffered solution including betaine, dimethyl sulfoxide (DMSO), ethyleneglycol, formamide, or a mixture thereof. In embodiments, the denaturantis a buffered solution including about 0% to about 50% dimethylsulfoxide (DMSO); about 0% to about 50% ethylene glycol; about 0% toabout 20% formamide; or about 0 to about 3M betaine, or a mixturethereof. In embodiments, the reaction conditions include incubation in adenaturant, wherein the denaturant is a buffered solution includingabout 15% to about 50% dimethyl sulfoxide (DMSO); about 15% to about 50%ethylene glycol; about 10% to about 20% formamide; or about 0 to about3M betaine, or a mixture thereof.

In embodiments, the first adapter is a hairpin adapter, and thedisplacing at least a portion of one strand of the double-strandednucleic acid comprises: (i) hybridizing a primer within a loop of thehairpin adapter, and (ii) in a primer extension reaction, extending theprimer with a strand-displacing polymerase. In embodiments, the firstadapter hairpin is the same as the second adapter hairpin. Inembodiments, the first adapter hairpin is different from the secondadapter hairpin.

In embodiments, the displacing at least a portion of one strand of thedouble-stranded nucleic acid comprises (i) forming a complex comprisinga portion of the double-stranded nucleic acid, a primer, and ahomologous recombination complex comprising a recombinase, (ii)releasing the recombinase, and (iii) in a primer extension reaction,extending the primer with a strand-displacing polymerase. Inembodiments, the complex comprises a helicase-polymerase fusion protein,such as DNA polymerase theta. Non-limiting examples are described byNewman et al., Structure, 2015, Dec. 1, 23(12), 2319-2330; and Guilliamet al., Nucleic Acids Res., 2015, Aug. 18, 43(14), 6651-64; which areincorporated herein by reference.

In embodiments, the displacing at least a portion of one strand of thedouble-stranded nucleic acid comprises forming a complex comprising aportion of the double-stranded nucleic acid, the probe oligonucleotide,and a homologous recombination complex comprising a recombinase, and thestep of hybridizing the probe oligonucleotide comprises releasing therecombinase.

In embodiments, the homologous recombination complex further comprises aloading factor, a single-stranded binding (SSB) protein, or both. Inembodiments, the recombinase reaction further includes a crowdingfactor, such as a dextran and PET, and ATP. In embodiments, the crowdingfactor includes poly(ethylene glycol) (PEG), polyvinylpyrrolidone (PVP),bovine serum albumin (BSA), dextran, Ficoll (e.g., Ficoll 70 or Ficoll400), glycerol, or a combination thereof. In embodiments, the crowdingagent is poly(ethylene glycol) (e.g., PEG 200, PEG 600, PEG 800, PEG2,050, PEG 4,600, PEG 6,000, PEG 8,000, PEG 10,000, PEG 20,000, or PEG35,000), dextran sulfate, bovine pancreatic trypsin inhibitor (BPTI),ribonuclease A, lysozyme, β-lactoglobulin, hemoglobin, bovine serumalbumin (BSA), or poly(sodium 4-styrene sulfonate) (PSS). Inembodiments, the crowding agent is PEG 200, PEG 600, PEG 800, PEG 2,050,PEG 4,600, PEG 6,000, PEG 8,000, PEG 10,000, PEG 20,000, or PEG 35,000.In embodiments, the crowding agent is PEG 10,000, PEG 20,000, or PEG35,000

In embodiments, the recombinase is a T4 UvsX, RecA, or Rad51 protein. Inembodiments, the recombinase is a T4 UvsX protein. In embodiments, therecombinase is a RecA protein. In embodiments, the recombinase is aRad51 protein. In embodiments, the homologous recombination complexfurther includes a loading factor, a single-stranded binding (SSB)protein, or both. In embodiments, the homologous recombination complexincludes a single-stranded binding (SSB) protein. In embodiments, theSSB protein is T4 gp32 protein, SSB protein, Extreme ThermostableSingle-Stranded DNA Binding Protein (ET-SSB), T7 gene 2.5 SSB protein,Thermococcus kodakarensis (KOD) SSB, Thermus thermophilus (TTH) SSB,Sulfolobus solfataricus (SSO) SSB, or phi29 SSB protein

In embodiments, the loading factor comprises a T4 UvsY protein.

In embodiments, the displacing at least a portion of one strand of thedouble-stranded nucleic acid includes exposing the double-strandednucleic acid to denaturing conditions. Non-limiting examples ofdenaturing conditions include increasing the temperature, changing thepH, adding chemical denaturants (e.g., NaOH). Suitable denaturingconditions, for example sodium hydroxide solution, formamide solution orheat, will be apparent to the skilled reader with reference to standardmolecular biology protocols (Sambrook et al., 2001, Molecular Cloning, ALaboratory Manual, 3rd Ed, Cold Spring Harbor Laboratory Press, ColdSpring Harbor Laboratory Press, NY; Current Protocols, eds Ausubel etal.). In embodiments, the displacing at least a portion of one strand ofthe double-stranded nucleic acid includes incubation with asingle-stranded binding (SSB) protein. In embodiments, the SSB is T4gp32 protein, SSB protein, T7 gene 2.5 SSB protein, or phi29 SSBprotein, Thermococcus kodakarensis (KOD) SSB, Thermus thermophilus (TTH)SSB, Sulfolobus solfataricus (SSO) SSB, or Extreme ThermostableSingle-Stranded DNA Binding Protein (ET-SSB). In embodiments, the SSB isactive (i.e., has measurable activity) at temperatures less than about72° C. In embodiments, the SSB is active (i.e., has measurable activity)at temperatures about 72° C. In embodiments, the SSB is active (i.e.,has measurable activity) at temperatures greater than about 72° C.

In embodiments, the probe oligonucleotide is covalently attached to asolid substrate. In embodiments, the solid substrate is in the form of achip, a bead, a well, a capillary tube, a slide, a wafer, a filter, afiber, a porous media, or a column. In embodiments, the solid substrateis gold, quartz, silica, plastic, glass, diamond, silver, metal, orpolypropylene. In embodiments, the solid substrate is porous. Inembodiments, the probe oligonucleotide is covalently attached to a bead.

In embodiments, the probe oligonucleotide is labeled with a first memberof a binding pair, and the step of separating the probe-hybridizeddouble-stranded nucleic acid comprises capturing the probe with a secondmember of the binding pair. In embodiments, the binding pair is abinding pair as described with respect to other aspects disclosedherein, including with respect to methods of sequencing described above.

In embodiments, the first member of the binding pair is biotin and thesecond member of the binding pair is avidin or streptavidin, or thesecond member of the binding pair is biotin and the first member of thebinding pair is avidin or streptavidin. In embodiments, the first memberof the binding pair is biotin and the second member of the binding pairis avidin or streptavidin. In embodiments, the second member of thebinding is biotin and the first member of the binding pair is avidin orstreptavidin. In embodiments, a member of the binding pair is avidin. Inembodiments, a member of the binding pair is streptavidin.

In embodiments, the probe is complementary to 10, 15, 20, 25, 50, 75,120, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 10 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 10, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 15 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 15, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 20 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 20, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 25 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 25, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 50 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 50, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 75 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 75, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 120 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto 120, or more consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid.

In embodiments, the probe is complementary to about 15 to about 60consecutive nucleotides of the displaced portion of the double-strandednucleic acid. In embodiments, the probe is complementary to about 20 toabout 50 consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid. In embodiments, the probe is complementaryto about 30 to about 40 consecutive nucleotides of the displaced portionof the double-stranded nucleic acid.

In certain embodiments, where the first strand of the complex isavailable to rehybridize to the second strand of the complex (such as incertain embodiments where strand displacement relies on denaturingconditions), longer probes may be preferred, such as probes that arecomplementary to 100, 120, or more consecutive nucleotides of thedisplaced portion of the double-stranded nucleic acid.

In embodiments, the double-stranded nucleic acid is a cell-free DNA(cfDNA) or circulating tumor DNA (ctDNA). In embodiments, thedouble-stranded nucleic acid is a cell-free DNA (cfDNA). In embodiments,the double-stranded nucleic acid is a circulating tumor DNA (ctDNA). Inembodiments, the double-stranded nucleic acid is from a FFPE sample. Inembodiments, the double-stranded nucleic acid is extracted from plasmaor from peripheral blood mononuclear cells (PBMCs). In embodiments, thedouble-stranded nucleic acid is 50 to 100 bp in length. In embodiments,the double-stranded nucleic acid includes genomic DNA, complementary DNA(cDNA), cell-free DNA (cfDNA), messenger RNA (mRNA), transfer RNA(tRNA), ribosomal RNA (rRNA), cell-free RNA (cfRNA), or noncoding RNA(ncRNA).

In embodiments, a plurality of different probe oligonucleotides areutilized during the hybridizing step, such that multiple targetpolynucleotides having different sequences are processed simultaneously.

In embodiments, the sequencing comprises sequencing according to any ofthe aspects described herein, including with respect to methods ofsequencing described above.

IV. Compositions and Kits

In certain embodiments, presented herein are compositions for conductinga method described herein, and including one or more elements thereof.In some embodiments, a composition comprises (i) a template nucleic acidcomprising sequences of a first strand of a Y-adapter, a forward strand(e.g., a first strand) of the double stranded nucleic acid, a hairpinadapter, a reverse strand (e.g., second strand) of the double strandednucleic acid and a second strand of the Y-adapter arranged in a 5′ to 3′direction; wherein the template is attached to a substrate. Inembodiments, the composition includes (ii) a primer hybridized to a loopof the hairpin adapter; wherein the template is attached to a substrate.In some embodiments, the substrate is a surface of a flow cell. In someembodiments, the substrate is a polymer coated surface of a flow cell.In embodiments, the composition includes the complement of the templatenucleic acid comprising sequences of a first strand of a Y-adapter, aforward strand (e.g., a first strand) of the double stranded nucleicacid, a hairpin adapter, a reverse strand (e.g., second strand) of thedouble stranded nucleic acid and a second strand of the Y-adapterarranged in a 5′ to 3′ direction wherein the complement of the templateis attached to a substrate. In embodiments, the substrate includes aglass surface including a polymer coating. In embodiments, the substrateis glass or quartz, such as a microscope slide, having a surface that isuniformly silanized. This may be accomplished using conventionalprotocols, such as those described in Beattie et a (1995), MolecularBiotechnology, 4: 213. Such a surface is readily treated to permitend-attachment of oligonucleotides (e.g., forward and reverse primers)prior to amplification. In embodiments the substrate surface furtherincludes a polymer coating, which contains functional groups capable ofimmobilizing primers. In some embodiments, the substrate includes apatterned surface suitable for immobilization of primers in an orderedpattern. A patterned surface refers to an arrangement of differentregions in or on an exposed layer of a substrate. For example, one ormore of the regions can be features where one or more primers arepresent. The features can be separated by interstitial regions wherecapture primers are not present. In some embodiments, the pattern can bean x-y format of features that are in rows and columns. In someembodiments, the pattern can be a repeating arrangement of featuresand/or interstitial regions. In some embodiments, the pattern can be arandom arrangement of features and/or interstitial regions. In someembodiments, the primers are randomly distributed upon the substrate. Insome embodiments, the primers are distributed on a patterned surface.

In certain embodiments, presented herein is a kit for sequencing doublestranded nucleic acid, in accordance with any of the methods describedherein, and including one or more elements thereof. In embodiments, thekit comprises: (i) a first adapter, wherein the first adapter comprisesa double-stranded portion and at least one single-stranded portion; (ii)a second adapter, wherein the second adapter is a hairpin adaptercomprising a nucleic acid having a 5′-end, a 5′-portion, a loop, a3′-portion and a 3′-end, and the 5′-portion of the hairpin adapter issubstantially complementary to the 3′-portion of the hairpin adapter;(iii) a first primer having a nucleic acid sequence complementary to aportion of the first adapter, or a complement thereof; and (iv) a secondprimer having a nucleic acid sequence complementary to the loop of thehairpin adapter, or a complement thereof. In certain embodiments, thefirst adapter is a Y-adapter, where the Y-adapter comprises (i) a firststrand having a 5′-portion and a 3′-portion, and (ii) a second strandhaving a 5′-portion and a 3′-portion, and the 3′-portion of the firststrand is substantially complementary to the 5′-portion of the secondstrand, and the 5′-portion of the first strand is not substantiallycomplementary to the 3′-portion of the second strand.

In embodiments, the kit includes at least a supply of a Y adapter asdefined herein, a hairpin adapter, and a supply of at least oneamplification primer which is capable of annealing to the Y adapter andpriming synthesis of an extension product, and a supply of at least oneamplification primer which is capable of annealing to the hairpinadapter and priming synthesis of an extension product.

The structure and properties of amplification primers will be well knownto those skilled in the art. Suitable primers of appropriate nucleotidesequence for use with the adapters included in the kit can be readilyprepared using standard automated nucleic acid synthesis equipment andreagents in routine use in the art. The kit may include as supply of onesingle type of primer or separate supplies (e.g., a mixture) of twodifferent primers, for example a pair of PCR primers suitable for PCRamplification of templates modified with the adapters (e.g., Y adapter,hairpin adapter, or both adapters) in solution phase and/or on asuitable solid support (i.e. solid-phase PCR).

Adapters and/or primers may be supplied in the kits ready for use, ormore preferably as concentrates-requiring dilution before use, or evenin a lyophilized or dried form requiring reconstitution prior to use. Ifrequired, the kits may further include a supply of a suitable diluentfor dilution or reconstitution of the primers. Optionally, the kits mayfurther comprise supplies of reagents, buffers, enzymes, and dNTPs foruse in carrying out nucleic acid amplification. Further components whichmay optionally be supplied in the kit include sequencing primerssuitable for sequencing templates prepared using the methods describedherein. In embodiments, the kit further includes instructions.

In an aspect is provided an isolated nucleic acid comprising a nucleicacid template. In embodiments, the nucleic acid template comprises adouble stranded nucleic acid (e.g., cfDNA molecule), a first adapterligated to a first end of the double stranded nucleic acid, and a secondadapter ligated to a second end of the double stranded nucleic acid,wherein the second adapter is a hairpin adapter. In embodiments, lessthan 50%, 60%, 70%, 80%, or 90% of the cytosines in the first or secondadapter are methylated cytosines. In embodiments, about 50% of thecytosines in the first or second adapter are methylated cytosines. Inembodiments, less than 50%, 60%, 70%, 80%, or 90% of the cytosines inthe first adapter are methylated cytosines. In embodiments, about 50% ofthe cytosines in the first adapter are methylated cytosines. Inembodiments, less than 50%, 60%, 70%, 80%, or 90% of the cytosines inthe hairpin adapter are methylated cytosines. In embodiments, about 50%of the cytosines in the hairpin adapter are methylated cytosines. Inembodiments, the first adapter includes a bisulfite conversion controlregion. In embodiments, the first adapter includes one or moreunmethylated cytosines. In embodiments, the second adapter includes abisulfite conversion control region. In embodiments, the second adapterincludes one or more unmethylated cytosines. In embodiments, the firstadapter includes one or more consecutive unmethylated cytosines. Inembodiments, the second adapter includes one or more consecutiveunmethylated cytosines.

V. Methods for Methylation and Mutational Analyses

In an aspect is provided a method of detecting methylation of a cytosinein a nucleic acid. In embodiments, the method includes sequencing adouble stranded nucleic acid including one or more methylated cytosines,the method including: (a) ligating a first adapter to a first end of thedouble stranded nucleic acid, and ligating a second adapter to a secondend of the double stranded nucleic acid, wherein the second adapter is ahairpin adapter, thereby forming a nucleic acid template; (b) convertingone or more cytosines (e.g., a methylated cytosine or a non-methylatedcytosine) to uracil; (c) annealing a first primer to the nucleic acidtemplate, wherein the first primer includes a sequence that iscomplementary to a portion of the first adapter, or a complementthereof; (d) sequencing a first portion of the nucleic acid template byextending the first primer, thereby generating a first read including afirst nucleic acid sequence of at least a first portion of the doublestranded nucleic acid; (e) annealing a second primer to the nucleic acidtemplate, wherein the second primer includes a sequence that iscomplementary to a sequence within a loop or stem of the hairpinadapter, or a complement thereof; and (f) sequencing a second portion ofthe nucleic acid template by extending the second primer, therebygenerating a second read including a nucleic acid sequence of at least asecond portion of the double stranded nucleic acid. In embodiments,converting one or more cytosines includes converting one or moremethylated-cytosines. In embodiments, converting one or more cytosinesincludes converting one or more methylated-cytosines using TET-assistedpyridine borane methods known in the art and/or described herein. Inembodiments, converting one or more cytosines includes converting one ormore nonmethylated-cytosines using bisulfate conversion or enzymaticconversion methods known in the art and/or described herein.

In embodiments, the first adapter includes one or more methylatedcytosines. In embodiments, the second adapter includes one or moremethylated cytosines. In embodiments, the first adapter includes aconsecutive sequence of methylated cytosines. In embodiments, the secondadapter includes a consecutive sequence of methylated cytosines.

In embodiments, the method includes converting one or more cytosines touracil. In embodiments, converting the one or more cytosines to uracilincludes chemical or enzymatic conversion. Chemical reagents that can beused to distinguish between methylated and non-methylated CpGdinucleotide sequences include for example, hydrazine, which cleaves thenucleic acid, and bisulfite treatment. Bisulfite treatment followed byalkaline hydrolysis specifically converts non-methylated cytosine touracil, leaving 5-methylcytosine unmodified. In embodiments, the methodincludes converting the one or more cytosines to uracil by contactingthe nucleic acid template with sodium bisulfite. Cytosine reacts withthe bisulfite ion to form a sulfonated cytosine reaction intermediatewhich is susceptible to deamination, giving rise to a sulfonated uracil.The sulfonate group can be removed under alkaline conditions, resultingin the formation of uracil. Alternatively, conversion may beaccomplished using restriction enzymes, such as HpaII and MspI, whichrecognize the sequence CCGG.

A method for bisulfite-free direct detection of 5-methylcytosine (5mC)and 5-hydroxymethylcytosine (5hmC) has been described (Liu Y et al. Nat.Biotechnol. 2019, 37(4)424-429, which is incorporated herein byreference), which combines ten-eleven translocation (TET) enzymaticoxidation of 5mC and 5hmC to 5-carboxylcytosine (5caC) with pyridineborane reduction of 5caC to dihydrouracil (DHU). Another bisulfite-freeapproach for methylation analysis is the NEBNext® Enzymatic Methyl-seqproduct, which first protects 5mC and 5hmC from deamination by TET2 andan oxidation enhancer, followed by APOBEC deamination of unprotectedcytosines to uracils.

In another aspect is provided a method of sequencing a single-strandednucleic acid including one or more methylated cytosines, the methodincluding: (a) ligating the 5′ end of a hairpin adapter to a first endof the single-stranded nucleic acid; and extending the 3′ end of thehairpin adapter with one or more polymerases in an amplificationreaction mixture including a plurality of conversion-resistant cytosineanalogue, to create a complementary strand hybridized to thesingle-stranded nucleic acid; (b) ligating a second adapter to the to asecond end of the single-stranded nucleic acid, thereby forming anucleic acid template; (c) converting one or more cytosines to uracil;(d) annealing a first primer to the nucleic acid template, wherein thefirst primer includes a sequence that is complementary to a portion ofthe second adapter, or a complement thereof; (e) sequencing a firstportion of the nucleic acid template by extending the first primer,thereby generating a first read including a first nucleic acid sequenceof at least a first portion of the single-stranded nucleic acid; (f)annealing a second primer to the nucleic acid template, wherein thesecond primer includes a sequence that is complementary to a sequencewithin a loop or stem of the hairpin adapter, or a complement thereof;and (g) sequencing a second portion of the nucleic acid template byextending the second primer, thereby generating a second read includinga nucleic acid sequence of at least a portion of the complementarystrand of the single-stranded nucleic acid. In embodiments, theconversion-resistant cytosine analogue is selected from the groupconsisting of: 5-hydroxymethylcytosine, 5-formylcytosine (5fC), 5-ethyldCTP, 5-methyl dCTP, 5-fluoro dCTP, 5-bromo dCTP, 5-iodo dCTP, 5-chlorodCTP, 5-trifluoromethyl dCTP, and 5-aza dCTP.

In another aspect is a method of detecting a single-nucleotidepolymorphism (SNP) or a single-nucleotide variant (SNV) in adouble-stranded nucleic acid. One unresolved problem with bisulfiteconversion is that it is often difficult to distinguish between SNPs orunmethylated cytosine in the same double stranded nucleic acid. This isespecially difficult for C>T SNPs, which is the most common substitution(>60%) in human population. Often this requires very high sequencingdepth to discern simultaneous SNVs, SNPs, and methylation profiles. Forexample, computational methods have been developed to predict germlineSNPs in bulk sequencing and suggest that at least 30× genomic coverageis required to identify 96% of SNPs from bisulfite converted DNA. Usingmethods described herein, e.g., generating the Y-template-hairpinconstructs, and obtaining sequencing information from both strandspermits identification of a SNP and a methylation profile. Inembodiments, the methods described herein reduce sequencing overheadwith higher accuracy for ctDNA. Methods described herein alsodifferentiate SNV and methylation simultaneously, at low sequencingdepths for germline mutations.

In embodiments, the method includes detecting SNVs and methylationstatus from a double stranded nucleic acid. Although SNVs can determineif a mutation occurred, it cannot reveal tissue of origin. Methylationis highly tissue specific and can be used to predict tissue of origin ofcfDNA. Current studies have shown common methylation CpG sites that aredifferentially methylated depending on tissue. By searching for thesedifferent methylation signals within ctDNA, one could determine if thereare elevated levels of certain tissue signals within the plasma.

In an aspect is provided a method of detecting a disease in a subject.In embodiments, the method includes obtaining a sample that includes adouble-stranded nucleic acid from the subject; identifying whether adisease is present in the sample by sequencing the sample according tothe methods described herein, and detecting a disease in a subject whenthe presence of a disease is identified in the sample. In another aspectis provided a method of diagnosing a subject with a disease. Inembodiments, the method includes obtaining a sample that includes adouble-stranded nucleic acid from the subject; identifying whether adisease is present in the sample by sequencing the sample according tothe methods described herein, and diagnosing a subject with a diseasewhen the presence of a disease is identified in the sample. In someembodiments, the disease is an autoimmune disease, hereditary disease,or cancer.

In embodiments, the disease is an autoimmune disease. In embodiments,the autoimmune disease is arthritis, rheumatoid arthritis, psoriaticarthritis, juvenile idiopathic arthritis, multiple sclerosis, systemiclupus erythematosus (SLE), myasthenia gravis, juvenile onset diabetes,diabetes mellitus type 1, Guillain-Barre syndrome, Hashimoto'sencephalitis, Hashimoto's thyroiditis, ankylosing spondylitis,psoriasis, Sjogren's syndrome, vasculitis, glomerulonephritis,auto-immune thyroiditis, Behcet's disease, Crohn's disease, ulcerativecolitis, bullous pemphigoid, sarcoidosis, ichthyosis, Gravesophthalmopathy, inflammatory bowel disease, Addison's disease, Vitiligo,asthma, allergic asthma, acne vulgaris, celiac disease, chronicprostatitis, inflammatory bowel disease, pelvic inflammatory disease,reperfusion injury, ischemia reperfusion injury, stroke, sarcoidosis,transplant rejection, interstitial cystitis, atherosclerosis,scleroderma, or atopic dermatitis. In embodiments, the autoimmunedisease is Achalasia, Addison's disease, Adult Still's disease,Agammaglobulinemia, Alopecia areata, Amyloidosis, Ankylosingspondylitis, Anti-GBM/Anti-TBM nephritis, Antiphospholipid syndrome,Autoimmune angioedema, Autoimmune dysautonomia, Autoimmuneencephalomyelitis, Autoimmune hepatitis, Autoimmune inner ear disease(AIED), Autoimmune myocarditis, Autoimmune oophoritis, Autoimmuneorchitis, Autoimmune pancreatitis, Autoimmune retinopathy, Autoimmuneurticaria, Axonal & neuronal neuropathy (AMAN), Baló disease, Behcet'sdisease, Benign mucosal pemphigoid, Bullous pemphigoid, Castlemandisease (CD), Celiac disease, Chagas disease, Chronic inflammatorydemyelinating polyneuropathy (CIDP), Chronic recurrent multifocalosteomyelitis (CRMO), Churg-Strauss Syndrome (CSS) or EosinophilicGranulomatosis (EGPA), Cicatricial pemphigoid, Cogan's syndrome, Coldagglutinin disease, Congenital heart block, Coxsackie myocarditis, CRESTsyndrome, Crohn's disease, Dermatitis herpetiformis, Dermatomyositis,Devic's disease (neuromyelitis optica), Discoid lupus, Dressler'ssyndrome, Endometriosis, Eosinophilic esophagitis (EoE), Eosinophilicfasciitis, Erythema nodosum, Essential mixed cryoglobulinemia, Evanssyndrome, Fibromyalgia, Fibrosing alveolitis, Giant cell arteritis(temporal arteritis), Giant cell myocarditis, Glomerulonephritis,Goodpasture's syndrome, Granulomatosis with Polyangiitis, Graves'disease, Guillain-Barre syndrome, Hashimoto's thyroiditis, Hemolyticanemia, Henoch-Schonlein purpura (HSP), Herpes gestationis or pemphigoidgestationis (PG), Hidradenitis Suppurativa (HS) (Acne Inversa),Hypogammalglobulinemia, IgA Nephropathy, IgG4-related sclerosingdisease, Immune thrombocytopenic purpura (ITP), Inclusion body myositis(IBM), Interstitial cystitis (IC), Juvenile arthritis, Juvenile diabetes(Type 1 diabetes), Juvenile myositis (JM), Kawasaki disease,Lambert-Eaton syndrome, Leukocytoclastic vasculitis, Lichen planus,Lichen sclerosus, Ligneous conjunctivitis, Linear IgA disease (LAD),Lupus, Lyme disease chronic, Meniere's disease, Microscopic polyangiitis(MPA), Mixed connective tissue disease (MCTD), Mooren's ulcer,Mucha-Habermann disease, Multifocal Motor Neuropathy (MMN) or MMNCB,Multiple sclerosis, Myasthenia gravis, Myositis, Narcolepsy, NeonatalLupus, Neuromyelitis optica, Neutropenia, Ocular cicatricial pemphigoid,Optic neuritis, Palindromic rheumatism (PR), PANDAS, Paraneoplasticcerebellar degeneration (PCD), Paroxysmal nocturnal hemoglobinuria(PNH), Parry Romberg syndrome, Pars planitis (peripheral uveitis),Parsonage-Turner syndrome, Pemphigus, Peripheral neuropathy, Perivenousencephalomyelitis, Pernicious anemia (PA), POEMS syndrome, Polyarteritisnodosa, Polyglandular syndromes type I, II, III, Polymyalgia rheumatica,Polymyositis, Postmyocardial infarction syndrome, Postpericardiotomysyndrome, Primary biliary cirrhosis, Primary sclerosing cholangitis,Progesterone dermatitis, Psoriasis, Psoriatic arthritis, Pure red cellaplasia (PRCA), Pyoderma gangrenosum, Raynaud's phenomenon, ReactiveArthritis, Reflex sympathetic dystrophy, Relapsing polychondritis,Restless legs syndrome (RLS), Retroperitoneal fibrosis, Rheumatic fever,Rheumatoid arthritis, Sarcoidosis, Schmidt syndrome, Scleritis,Scleroderma, Sjogren's syndrome, Sperm & testicular autoimmunity, Stiffperson syndrome (SPS), Subacute bacterial endocarditis (SBE), Susac'ssyndrome, Sympathetic ophthalmia (SO), Takayasu's arteritis, Temporalarteritis/Giant cell arteritis, Thrombocytopenic purpura (TTP), Thyroideye disease (TED), Tolosa-Hunt syndrome (THS), Transverse myelitis, Type1 diabetes, Ulcerative colitis (UC), Undifferentiated connective tissuedisease (UCTD), Uveitis, Vasculitis, Vitiligo, or Vogt-Koyanagi-HaradaDisease.

In embodiments the disease is a hereditary disease. In embodiments, thehereditary disease is cystic fibrosis, alpha-thalassemia,beta-thalassemia, sickle cell anemia (sickle cell disease), Marfansyndrome, fragile X syndrome, Huntington's disease, or hemochromatosis.

In embodiments the disease is a cancer. As used herein, the term“cancer” refers to all types of cancer, neoplasm or malignant tumorsfound in mammals (e.g., humans), including leukemia, carcinomas andsarcomas. Exemplary cancers that may be treated with a compound ormethod provided herein include brain cancer, glioma, glioblastoma,neuroblastoma, prostate cancer, colorectal cancer, pancreatic cancer,cervical cancer, gastric cancer, ovarian cancer, lung cancer, and cancerof the head. Exemplary cancers that may be treated with a compound ormethod provided herein include cancer of the thyroid, endocrine system,brain, breast, cervix, colon, head & neck, liver, kidney, lung,non-small cell lung, melanoma, mesothelioma, ovary, sarcoma, stomach,uterus, Medulloblastoma, colorectal cancer, pancreatic cancer.Additional examples include, Hodgkin's Disease, Non-Hodgkin's Lymphoma,multiple myeloma, neuroblastoma, glioma, glioblastoma multiforme,ovarian cancer, rhabdomyosarcoma, primary thrombocytosis, primarymacroglobulinemia, primary brain tumors, cancer, malignant pancreaticinsulanoma, malignant carcinoid, urinary bladder cancer, premalignantskin lesions, testicular cancer, lymphomas, thyroid cancer,neuroblastoma, esophageal cancer, genitourinary tract cancer, malignanthypercalcemia, endometrial cancer, adrenal cortical cancer, neoplasms ofthe endocrine or exocrine pancreas, medullary thyroid cancer, medullarythyroid carcinoma, melanoma, colorectal cancer, papillary thyroidcancer, hepatocellular carcinoma, or prostate cancer. In embodiments,the cancer is breast cancer, lung cancer, prostate cancer, colorectalcancer, renal cancer, uterine cancer, pancreatic cancer, cancer of theesophagus, a lymphoma, head/neck cancer, ovarian cancer, a hepatobiliarycancer, a melanoma, cervical cancer, multiple myeloma, leukemia, thyroidcancer, bladder cancer, gastric cancer, or a combination thereof. Inembodiments, the cancer is a predefined stage of a breast cancer, apredefined stage of a lung cancer, a predefined stage of a prostatecancer, a predefined stage of a colorectal cancer, a predefined stage ofa renal cancer, a predefined stage of a uterine cancer, a predefinedstage of a pancreatic cancer, a predefined stage of a cancer of theesophagus, a predefined stage of a lymphoma, a predefined stage of ahead/neck cancer, a predefined stage of a ovarian cancer, a predefinedstage of a hepatobiliary cancer, a predefined stage of a melanoma, apredefined stage of a cervical cancer, a predefined stage of a multiplemyeloma, a predefined stage of a leukemia, a predefined stage of athyroid cancer, a predefined stage of a bladder cancer, or a predefinedstage of a gastric cancer. In some embodiments, the cancer is apredefined subtype of a cancer. In certain instances, the cancer isearly stage cancer. In other instances, the cancer is late stage cancer.

In embodiments, the subject is suspected of having a genetic variationor a disease or condition associated with a genetic variation (e.g., anoncogene). In embodiments, the sample, and/or the oncogene includes oneor more mutations in one or more of the genes TP53, PIK3CA, PTEN, APC,VHL, KRAS, MLL3, MLL2, ARID1A, PBRM1, NAV3, EGFR, NF1, PIK3R1, CDKN2A,GATA3, RB1, NOTCH1, FBXW7, CTNNB1, DNMT3A, MAP3K1, FLT3, MALAT1, TSHZ3,KEAP1, CDH1, ARHGAP35, CTCF, NFE2L2, SETBP1, BAP1, NPM1, RUNX1, NRAS,IDH1, TBX3, MAP2K4, RPL22, STK11, CRIPAK, CEBPA, KDM6A, EPHA3, AKT1,STAG2, BRAF, AR, AJUBA, EPPK1, TSHZ2, PIK3CG, SOX9, ATM, CDKN1B, WT1,HGF, KDMSC, PRX, ERBB4, MTOR, TLR4, U2AF1, ARIDSB, TET2, ATRX, MLL4,ELF3, BRCA1, LRRK2, POLQ, FOXA1, IDH2, CHEK2, KIT, HIST1H1C, SETD2,PDGFRA, EP300, FGFR2, CCND1, EPHB6, SMAD4, FOXA2, USP9X, BRCA2, NFE2L3,FGFR3, ASXL1, TGFBR2, SOX17, CDKN1A, B4GALT3, SF3B1, TAF1, PPP2R1A,CBFB, ATR, SIN3A, VEZF1, HIST1H2BD, EIF4A2, CDK12, PHF6, SMC1A, PTPN11,ACVR1B, MAPK8IP1, H3F3C, NSD1, TBL1XR1, EGR3, ACVR2A, MECOM, LIFR, SMC3,NCOR1, RPL5, SMAD2, SPOP, AXIN2, MIR142, RAD21, ERCC2, CDKN2C, EZH2, orPCBP1. In embodiments, the cancer is lung cancer, colorectal cancer,skin cancer, colon cancer, pancreatic cancer, breast cancer, cervicalcancer, lymphoma, leukemia, or a cancer associated with aberrant K-Ras,aberrant APC, aberrant Smad4, aberrant p53, or aberrant TGFβ. Inembodiments, the cancer cell includes a ERBB2, KRAS, TP53, PIK3CA, orFGFR2 gene.

EXAMPLES Example 1: Linked Paired Strand Sequencing

Commercially available next-generation sequencing (NGS) technologiestypically require library preparation, whereby a pair of specificadapter sequences are ligated to the ends of DNA fragments in order toenable sequencing by the instrument. Typically, preparation of a nucleicacid library involves 5 steps: DNA fragmentation, polishing, adapterligation, size selection, and library amplification.

Fragmentation of DNA can be achieved by enzymatic digestion or physicalmethods (e.g., sonication, nebulization, or hydrodynamic shearing).Enzymatic digestion produces DNA ends that can be efficiently polishedand ligated to adapter sequences. However, it is difficult to controlthe enzymatic reaction and produce fragments of predictable length. Inaddition, enzymatic fragmentation is frequently base-specific thusintroducing representation bias into the sequence analysis.Alternatively, physical methods to fragment DNA are random and DNA sizedistribution can be more easily controlled, but DNA ends produced byphysical fragmentation are often damaged and a conventional polishingreaction may be insufficient to generate ample ligation-compatible ends.Typical polishing mixtures contain T4 DNA polymerase and T4polynucleotide kinase. These enzymes excise 3′ overhangs, fill in 3′recessed ends, and remove any potentially damaged nucleotides therebygenerating blunt ends on the nucleic acid fragments. The T4polynucleotide kinase used in the polishing mix adds a phosphate to the5′ ends of DNA fragments that can be lacking such, thus making themligation-compatible to NGS adapters.

Prior to ligation, adenylation of repaired nucleic acids using apolymerase which lacks 3′-5′ exonuclease activity is often performed inorder to minimize chimera formation and adapter-adapter (dimer) ligationproducts. In these methods, single 3′ A-overhang DNA fragments areligated to single 5′ T-overhang adapters, whereas A-overhang fragmentsand T-overhang adapters have incompatible cohesive ends forself-ligation. During size selection, fragments of undesired size areeliminated from the library using gel or bead-based selection in orderto optimize the library insert size for the desired sequencing readlength. This often maximizes sequence data output by minimizing overlapof paired end sequencing that occurs from short DNA library inserts.Amplifying libraries prior to NGS analysis is typically a beneficialstep to ensure there is a sufficient quantity of material to besequenced.

Linked Duplex Sequencing: Ligating Adaptors

In some aspects of a method herein, an adapter-target-adapter nucleicacid template (FIG. 1A and FIG. 1C) is provided where two non-identicaladapters are ligated to each respective end of a polynucleotide duplex.A general overview is provided in FIG. 1B and FIG. 1D. Embodiments ofadapters contemplated herein include those shown in FIGS. 2A-2B and FIG.4. A polynucleotide duplex refers to a double-stranded portion of apolynucleotide, for example a polynucleotide desired to be sequenced.

As depicted in FIG. 1B, a first adapter is a Y adapter (alternatively,this may be referred to as a mismatched adapter or a forked adapter)that is ligated to one end of a polynucleotide duplex. The adapter isformed by annealing two single-stranded oligonucleotides, hereinreferred to as P1 and P2′. P1 and P2′ may be prepared by a suitableautomated oligonucleotide synthesis technique. The oligonucleotides arepartially complementary such that a 3′ end and/or a 3′ portion of P1 iscomplementary to the 5′ end and/or a 5′ portion of P2′. A 5′ end and/ora 5′ portion of P1 and a 3′ end and/or a 3′ portion of P2′ are notcomplementary to each other, in certain embodiments. When the twostrands are annealed, the resulting Y adapter is double-stranded at oneend (the double-stranded region) and single-stranded at the other end(the unmatched region), and resembles a ‘Y’ shape.

The single-stranded portions (the unmatched regions) of both P1 and P2′have an elevated melting temperature (T_(m)) (e.g., about 75° C.)relative to their respective complements to enable efficient binding ofsurface primers and stable binding of sequencing primers. To achieve anelevated T_(m) in a reasonable length primer, the GC content isoften >50% (e.g., approximately 60-75% GC content). In contrast to thesingle-stranded portions, a double-stranded region, in certainembodiments, has a moderate T_(m) (e.g., 40-45° C.) so that it is stableduring ligation. In embodiments, a double-stranded region has anelevated T_(m) (e.g., 60-70° C.). In embodiments, the GC content of thedouble-stranded region is >50% (e.g., approximately 60-75% GC content).The unmatched region of P1 and P2′, in certain embodiments, are about25-35 nucleotides (e.g., 30 nucleotides), whereas the double-strandedregion is shorter, ranging about 10-20 nucleotides (e.g., 13nucleotides) in total. For example, P2′ may be a total of 43 nucleotidesin length, as shown in FIG. 2A. In embodiments, the P1 region of the Yadapter has the sequence S1 sequence (SEQ ID NO:1) and the P2′ region ofthe Y adapter has the S2 (SEQ ID NO:3) sequence, as described in Table 1below. In embodiments, the P1 region of the Y adapter has the sequenceS4 sequence (SEQ ID NO:2) and the P2′ region of the Y adapter has the S5(SEQ ID NO:4) sequence, as described in Table 1 below.

TABLE 1Sequences for the Y adapters. Note, the ′*′ is indicative of an optionalphosphorothioate linkage. Phosphorothioate linkages assist in protecting the oligonucleotideagainst exonuclease degradation from certain polymerases (e.g., phi29).P1 regions of the Y adapter S1 (SEQ ID NO: 1)ACAAAGGCAGCCACGCACTCCTTCCCT GAAGGCCGGAATC*T S4 (SEQ ID NO: 2)GCTGCCGCCACTAGCCATCTTACTGCT GAGGACTCTTCGC*T P2′ regions of the Y adapterS2 (SEQ ID NO: 3) /5Phos/GATTCCGGCCTTGTGGTTGGTGA GGGTCATCTCGCTGGAGS5 (SEQ ID NO: 4) /5Phos/GCGAAGAGTCCTGGAGTGCCGC CAATGTATGCGAGGGTGA

As shown in FIG. 3, the double-stranded region of the forked adapter maybe blunt-ended (top), it may have a 3′ overhang (middle), or a 5′overhang (bottom). The overhang may comprise a single nucleotide or morethan one nucleotide. The 5′ end of the double-stranded part of theforked adapter is phosphorylated, i.e. the 5′ end of P2′. The presenceof the 5′ phosphate group (referred to as 5′P in FIG. 3) allows theadapter to ligate to the polynucleotide duplex. The 5′ end of P1 may bebiotinylated or have a functional group at the end, thus enabling it tobe immobilized on a surface (e.g., a planar solid support).

Alternatively, as depicted in FIG. 1D, the first adapter is a hairpinadapter (e.g., the hairpin adapter of FIG. 2B) and it is ligated to oneend of a polynucleotide duplex.

The second adapter is a hairpin adapter (alternatively, it may bereferred to as a stem-loop adapter, barbell, or hairpin loop adapter)and it is ligated to one end of a polynucleotide duplex, depicted ascontaining a P3 priming site in FIG. 1C and FIG. 4. The hairpin adaptercomprises a double-stranded region which has a moderate T. (e.g., 40-45°C.) so that it is stable during ligation, and comprises at least 10nucleotides. The hairpin adapter also comprises a loop region which hasa primer sequence and has an elevated T. (e.g., 75° C.) relative to thedouble stranded region to enable stable binding of a complementarysequencing primer. The loop region or the stem region of the hairpin mayfurther comprise a barcode or Unique Molecular Identifier (UMI) usingdegenerate sequences. The UMI consists of 3-5 degenerate nucleotides.

TABLE 2Sequences for the hairpin adapter. Note, the ′*′ is indicative of an optionalphosphorothioate linkage. Phosphorothioate linkages assist in protecting the oligonucleotideagainst exonuclease degradation from certain polymerases (e.g., phi29).B1 (SEQ ID NO: 5) /5Phos/ GCGCGCG TTT TTT TTGCTTGCGTCTCCTGCCAGCCATATCCGGTCTACGTGATC C TTT TTT TT CGCGCGC*TB2 (SEQ ID NO: 6) /5Phos/GCGCGCGTTT TTT TTT TTT TTGCTTGCGTCTCCTGCCAGCCATATCCGGTCTACGTGATC C TTT TTT TTT TTT TT CGCGCGC*TB3 (SEQ ID NO: 7) /5Phos/GGATCACGTAGATTTTGCTTGCGTCTCCTGCCAGCCATATCCGGTTTTTCTACGTGATTCC*T B4 (SEQ ID NO: 8) /5Phos/GCGAAGAGTCCTS4S5′_in_loop_0Ts GGAGTGCCGCCAATGTATGCGAGGGTGAGCTGCCGCCACTAGCCATCTTACTGCTG AGGACTCTTCGC*T B5 (SEQ ID NO: 9)/5Phos/GCGAAGAGTCCT TTT TTT S4S5′_in loop_6TsGGAGTGCCGCCAATGTATGCGAGGGTGA GCTGCCGCCACTAGCCATCTTACTGCTG TTT TTTAGGACTCTTCGC*T B6 (SEQ ID NO: 10) /5Phos/GCGAAGAGTCCT TTT TTTS4S5′_in loop_6+8Ts GGAGTGCCGCCAATGTATGCGAGGGTGA TTT TTT TGCTGCCGCCACTAGCCATCTTACTGCTG TTT TTT AGGACTCTTCGC*T B7 (SEQ ID NO: 11)/5Phos/GATTCCGGCCTT S1S2′_in loop_0TsGTGGTTGGTGAGGGTCATCTCGCTGGAGACAAAGGCAG CCACGCACTCCTTCCCTGAAGGCCGGAATC*TB8 (SEQ ID NO: 12) /5Phos/GATTCCGGCCTT TTT TTT S1S2′_in loop_6TsGTGGTTGGTGAGGGTCATCTCGCTGGAGACAAAGGCAGCCACGCACTCCTTCCCTGTTTTTTAAGGCCGGAATC*T B9 (SEQ ID NO:13)/5Phos/GATTCCGGCCTT TTT TTT S1S2′_in loop_6+7TsGTGGTTGGTGAGGGTCATCTCGCTGGAGTTT TTTTACAAAGGCAGCCACGCACTCCTTCCCTG TTT TTT AAGGCCGGAATC*TB10 (SEQ ID NO: 14)  /5Phos/GGATCACGTAGATTTTGCTTGCGTCTCCTGCCAGCCATATCCGGTTTTTCTACGTGATCC*T B11 (SEQ ID NO: 15) 5Phos/GG ATC ACG TAG ATT TTT TTT TTT TGC TTG CGT B10+12TCTC CTG CCA GCC ATA TCC GGT TTT TTT TTT TTT CTA CGT GAT CC*TB12 (SEQ ID NO: 16) 5Phos/GG ATC ACG TAG ATT TTT TTT TTT TTT TTT TTTB10+24T TTT TGC TTG CGT CTC CTG CCA GCC ATA TCC GGTTTT TTT TTT TTT TTT TTT TTT TTT CTA CGT GAT CC*T B13 (SEQ ID NO: 17)5Phos/GG ATC ACG TAG ATT TTT TTT TTT TTT TTT TTT B10+40-10TTTT TTT TTT TTT TTT TTT TTG CTT GCG TCT CCT GCCAGC CAT ATC CGG TTT TTT TTT TTC TAC GTG ATC C*T B14 (SEQ ID NO: 18)/5Phos/GGA TCA CGT AGA TTT TAG ATC TGC TTG CGT B10 + clvCTC CTG CCA GCC ATA TCC GGT TTT TCT ACG TGA TCC* T B15 (SEQ ID NO: 19)/5Phos/GGA TCA CGT AGA TTTTTTTTTTTT AGA TCT B11 + clvGCT TGC GTC TCC TGC CAG CCA TAT CCG GTTTTTTTTTTTTC TAC GTG ATC C*T

In embodiments, a hairpin adapter comprises a sequence selected from SEQID NOs:5-17. In embodiments, the hairpin adapter has the B1 (SEQ IDNO:5) sequence described in Table 2. In embodiments, the hairpin adapterhas the B2 (SEQ ID NO:6) sequence described in Table 2. In embodiments,the hairpin adapter has the B3 (SEQ ID NO:7) sequence described in Table2. In embodiments, the hairpin adapter has the B4 (SEQ ID NO: 8)sequence described in Table 2. In embodiments, the hairpin adapter hasthe B5 (SEQ ID NO:9) sequence described in Table 2. In embodiments, thehairpin adapter has the B6 (SEQ ID NO:10) sequence described in Table 2.In embodiments, the hairpin adapter has the B7 (SEQ ID NO:11) sequencedescribed in Table 2. In embodiments, the hairpin adapter has the B8(SEQ ID NO:12) sequence described in Table 2. In embodiments, thehairpin adapter has the B9 (SEQ ID NO:13) sequence described in Table 2.In embodiments, the hairpin adapter has the B10 (SEQ ID NO:14) sequencedescribed in Table 2. In embodiments, the hairpin adapter has the B11(SEQ ID NO:15) sequence described in Table 2. In embodiments, thehairpin adapter has the B12 (SEQ ID NO:16) sequence described in Table2. In embodiments, the hairpin adapter has the B13 (SEQ ID NO:17)sequence described in Table 2. In embodiments, the hairpin adapter hasthe B13 (SEQ ID NO:18) sequence described in Table 2. In embodiments,the hairpin adapter has the B13 (SEQ ID NO:19) sequence described inTable 2.

As shown in FIG. 5, the double-stranded region of the hairpin adaptermay be blunt-ended (top), it may have a 5′ overhang (middle), or a 3′overhang (bottom). The overhang may comprise a single nucleotide or morethan one nucleotide. The 5′ end of the double-stranded part of thehairpin adapter is phosphorylated. The presence of the 5′ phosphategroup allows the adapter to ligate to the polynucleotide duplex.

The order of ligation events is not relevant, however for the purposesof discussion the terms ‘first’ and ‘second’ are used in reference tothe sequence in which the adapter is ligated to the polynucleotideduplex. It is understood that the ligation of the Y adapter or thehairpin adapter may occur first, such that the resultingadapter-target-adapter constructs contain non-identical adapters.

Note, during this step it is possible to form adapter dimers (i.e., twoadapters ligate together with no intervening template nucleic acid).There are several ways to reduce adapter dimer formation in the adapterligation NGS library preparation described herein, including i) astringent purification step (e.g., SPRI) after 3′ adapter ligation toremove non-ligated 3′ adapter molecules, prior to the second ligation ofthe 5′ adapter; ii) the use of A-tailed DNA and T-overhang adapters;iii) or utilizing alkaline phosphatase treatment after 3′ adapterligation, before any SPRI cleanup, to remove 5′ phosphate group from the3′ adapter to render any carryover 3′ adapter to be ligationincompatible and inert in the 5′ adapter ligation step.

Methods

Fragmented DNA may be made blunt-ended by a number of methods known tothose skilled in the art. In embodiments, the ends of the fragmented DNAare end repaired with T4 DNA polymerase and Klenow polymerase, aprocedure well known to those skilled in the art, and thenphosphorylated with a polynucleotide kinase enzyme. A single ‘A’deoxynucleotide is then added to both 3′ ends of the DNA molecules usingTaq polymerase enzyme, producing a one-base 3′ overhang that iscomplementary to the one-base T overhang on the double-stranded end ofthe Y adapter and hairpin adapter. For example, in the presence of a T4DNA ligase, an A overhang is created on both strands at the 3′ hydroxylend of a target duplex polynucleotide. For example, using Blunt/TALigase Master Mix (NEB #M0367) includes a T4 DNA ligase in a reactionbuffer and ligation enhancers to ensure efficient A tailing. It ispreferable to polish or use a filling reaction to ensure the ends of thetarget duplex polynucleotide are blunt before adding the A overhang.Examples of ends that need polishing or filling include insertsgenerated by shearing or sonication. A number of DNA polymerases willremove DNA overhangs and/or can be used to fill in missing bases ifthere is a 3′ hydroxyl available for priming. Polymerases for suchreactions include, but are not limited to, a T4 DNA polymerase, PFU, andthe Klenow Fragment of DNA polymerase I.

A ligation reaction between the Y adapter, the hairpin adapter, and theDNA fragments is then performed using a suitable ligase enzyme (e.g. T4DNA ligase) which joins one hairpin adapter and one Y adapter to eachDNA fragment, one at either end, to form adapter-target-adapterconstructs that somewhat resemble a bobby pin hair fastener (see FIG.1A). Alternatively, a ligation reaction between a first hairpin adapter(e.g., FIG. 2B), and a different second hairpin adapter (e.g., FIG. 4),and the DNA fragments is then performed using a suitable ligase enzyme(e.g. T4 DNA ligase) which joins the first hairpin adapter and thesecond hairpin adapter to each DNA fragment, one at either end, to formadapter-target-adapter constructs (see FIG. 1D).

The products of this reaction can be purified from leftover unligatedadapters that by a number of means (e.g., NucleoMag NGS Clean-up andSize Select kit, Solid Phase Reversible Immobilization (SPRI) beadmethods such as AMPureXP beads, PCRclean-dx kit, Axygen AxyPrepFragmentSelect-I Kit), including size-inclusion chromatography,preferably by electrophoresis through an agarose gel slab followed byexcision of a portion of the agarose that contains the DNA greater insize that the size of the adapter.

Linked Duplex Sequencing: Clustering Amplification.

Once formed, the library of adapter-target-adapter templates preparedaccording to the methods described above can be used for solid-phasenucleic acid amplification.

Thus, in another aspect is provided a method of nucleic acidamplification of template polynucleotide molecules which includespreparing a library of template polynucleotide molecules (e.g.,adapter-target-adapter templates) and performing an amplificationreaction (e.g., a solid-phase nucleic acid amplification reaction)wherein the template polynucleotide molecules are amplified. Inembodiments, the method includes providing a plurality of primers (e.g.,P1 and P2) that are immobilized on a solid substrate. Note, however, forclarity only a few immobilized primers are depicted in FIG. 6A.

An adapter-target-adapter construct (i.e., the denatured single strand,reading from 5′ to 3′ having the formula P1-template-P3-template-P2′generated according to the methods described herein) is hybridized to acomplementary primer (e.g., the complement to P2′, referred to as P2)that is immobilized on a solid substrate. In the presence of apolymerase (wherein the polymerase is not shown in FIG. 6A) the P2strand is extended to generate a complementary copy, wherein thedenatured single strand, reading from the 5′ to the 3′ has the formulaP1′-template-P3′-template-P2. The original adapter-target-adapter may beremoved. Because of the self-folding of the adapter-target-adapterconstruct, initially seeding on the solid surface could be done withoutadditional denaturation steps (e.g., as long as the products are in thehairpin state).

Next, the complementary copy is annealed to a P1 primer that isimmobilized on the solid substrate, which in the presence of a DNApolymerase (again, the polymerase is not shown in FIG. 6B) extends P1primer to reform the original adapter-target-adapter construct (i.e.,the denatured single strand having the formulaP1-template-P3-template-P2′) which then hybridizes with an immobilizedP2 primer. The products of the extension reaction (i.e. theP1-template-P3-template-P2′ hybridized to an immobilized P2, andP1′-template-P3′-template-P2 hybridized to P1) may be subjected tostandard denaturing conditions in order to separate the extensionproducts from strands of the adapter-target constructs. Theadapter-target-adapter constructs may then anneal to a complementaryimmobilized primer and may be extended in the presence of a polymerase.These steps, depicted in FIGS. 6A-6B, may be repeated one or more times,through rounds of primer annealing, extension and denaturation, in orderto form multiple copies of the same extension products containingadapter-target-adapter constructs, or the complements thereof. Note,this bridging amplification is typically more efficient than amplifyinglinear strands, because the adapter-target-adapter products self-fold,thus leaving the primer site accessible.

The term “solid-phase amplification” as used herein refers to anynucleic acid amplification reaction carried out on or in associationwith a solid support such that all or a portion of the amplifiedproducts are immobilized on the solid support as they are formed. Theterm encompasses solid-phase polymerase chain reaction (solid-phasePCR), which is a reaction analogous to standard solution phase PCR,except that both of the forward and reverse amplification primers(referred to herein as P1 and P2) are immobilized on the solid support.In practice, there will be a “plurality” of identical forward primersand/or a “plurality” of identical reverse primers immobilized on thesolid support, since the PCR process requires an excess of primers tosustain amplification.

In embodiments, amplification primers for solid-phase amplification arepreferably immobilized by covalent attachment to the solid support at ornear the 5′ end of the primer, leaving the template-specific portion ofthe primer free for annealing to the cognate template and the 3′hydroxyl group free for primer extension. Any suitable covalentattachment means known in the art may be used for this purpose. Theprimer itself may include a moiety, which may be a non-nucleotidechemical modification, to facilitate attachment. In embodiments, theprimer may include a sulfur-containing nucleophile (e.g.,phosphorothioate or thiophosphate) at the 5′ end.

In embodiments, the adapter-target-adapter templates prepared accordingto the methods described above can be used to prepare clustered arraysof nucleic acid colonies by solid-phase PCR amplification. The terms“cluster” and “colony” are used interchangeably herein to refer to adiscrete site on a solid support comprised of a plurality of immobilizednucleic acid strands and a plurality of immobilized complementarynucleic acid strands. The term “clustered array” refers to an arrayformed from such clusters or colonies. In this context the term “array”is not to be understood as requiring an ordered arrangement of clusters.

Linked Duplex Sequencing: Use in Sequencing

In another aspect is provided methods of sequencing amplified nucleicacids, optionally generated by the amplification methods describedherein. The method includes optionally removing all or a portion of oneimmobilized strand in a “bridged” double-stranded nucleic acid structure(i.e. linearizing) and sequencing.

The products of solid-phase amplification reactions described hereinwherein both P1 and P2 primers are covalently immobilized on the solidsurface are may be referred to as “bridged structures” formed byannealing of pairs of immobilized polynucleotide strands and immobilizedcomplementary strands, both strands being attached to the solid supportat the 5′ end.

Arrays comprised of such bridged structures provide inefficienttemplates for nucleic acid sequencing, since hybridization of aconventional sequencing primer to one of the immobilized strands is notpreferred compared to annealing of this strand to its immobilizedcomplementary strand under standard conditions for hybridization. Inorder to provide more suitable templates for nucleic acid sequencing itis preferred to remove substantially all or at least a portion of one ofthe immobilized strands in the “bridged” structure in order to generatea template which is at least partially single-stranded. The portion ofthe template which is single-stranded will thus be available forhybridization to a sequencing primer. The process of removing all or aportion of one immobilized strand in a “bridged” double-stranded nucleicacid structure may be referred to herein as “linearization”. Bridgedtemplate structures may be linearized by cleavage of one or both strandswith a restriction endonuclease or by cleavage of one strand with anicking endonuclease. Other methods of cleavage can be used as analternative to restriction enzymes or nicking enzymes, includingchemical cleavage (e.g. cleavage of a diol linkage with periodate),cleavage of abasic sites by cleavage with endonuclease, or by exposureto heat or alkali, cleavage of ribonucleotides incorporated intoamplification products otherwise comprised of deoxyribonucleotides,photochemical cleavage or cleavage of a peptide linker. Alternatively,the primers may be attached to the solid surface with a cleavablelinker, such that upon exposure to a cleaving agent, all or a portion ofthe primer is removed from the surface.

Linearization: To a solid surface having a plurality of extensionproducts generated according to the methods described above, the methodincludes optionally cleaving one of the immobilized primers (e.g., P1).To the remaining extended primers (e.g., P2), the strands are terminatedusing dideoxy nucleotides, as shown in FIG. 7A.

Sequencing reactions: The initiation point for the first sequencingreaction is provided by annealing of a sequencing primer complementaryto one of the strands in the Y adapter (e.g., P1), also shown in FIG.7A. FIG. 7B depicts the sequencing steps. In the presence of a stranddisplacing polymerase, nucleotides (e.g., labeled nucleotides) areincorporated and detected such that the identity of the incorporatednucleotides allow for the identification of the first template strand.Thus, the first sequencing reaction may include hybridizing a sequencingprimer to a region of a linearized amplification product, sequentiallyincorporating one or more nucleotides into a polynucleotide strandcomplementary to the region of amplified template strand to besequenced, identifying the base present in one or more of theincorporated nucleotide(s) and thereby determining the sequence of aregion of the template strand. Note, the first sequenced strand (i.e.,the first primer extension product) may be i) removed; 2) terminated(e.g., introducing dideoxy nucleotides); or iii) extended and ligated tothe hairpin adapter.

Next, a second sequencing reaction is initiated by annealing asequencing primer complementary to a region in the hairpin (e.g., P3),and in the presence of a strand displacing polymerase, nucleotides(e.g., labeled nucleotides) are incorporated and detected such that theidentity of the incorporated nucleotides allows for the identificationof the second template strand. Thus, the second sequencing reaction mayinclude hybridizing a sequencing primer to a region of a linearizedamplification product, sequentially incorporating one or morenucleotides into a polynucleotide strand complementary to the region ofamplified template strand to be sequenced, identifying the base presentin one or more of the incorporated nucleotide(s) and thereby determiningthe sequence of a region of the template strand.

Sequencing can be carried out using any suitable sequencing-by-synthesistechnique, wherein nucleotides are added successively to a free 3′hydroxyl group, resulting in synthesis of a polynucleotide chain in the5′ to 3′ direction. In embodiments, the identity of the nucleotide addedis determined after each nucleotide addition.

In embodiments, the sequencing method relies on the use of modifiednucleotides that can act as reversible reaction terminators. Once themodified nucleotide has been incorporated into the growingpolynucleotide chain complementary to the region of the template beingsequenced there is no free 3′-OH group available to direct furthersequence extension and therefore the polymerase cannot add furthernucleotides. Once the identity of the base incorporated into the growingchain has been determined, the 3′ reversible terminator may be removedto allow addition of the next successive nucleotide. Such reactions canbe done in a single experiment if each of the modified nucleotides has adifferent label attached thereto, known to correspond to the particularbase, to facilitate discrimination between the bases added at eachincorporation step. Alternatively, a separate reaction may be carriedout containing each of the modified nucleotides separately.

The modified nucleotides may carry a label (e.g., a fluorescent label)to facilitate their detection. Each nucleotide type may carry adifferent fluorescent label. However, the detectable label need not be afluorescent label. For example, the detectable label can be aparamagnetic spin label such as nitroxide, and detected by electronparamagnetic resonance and related techniques. Exemplary spin labels andtechniques for their detection are described in Hubbell et al. TrendsBiochem Sci. 27:288-95 (2002), which is incorporated herein by referencein its entirety. Any label can be used which allows the detection of anincorporated nucleotide. One method for detecting fluorescently labelednucleotides includes using laser light of a wavelength specific for thelabeled nucleotides, or the use of other suitable sources ofillumination. The fluorescence from the label on the nucleotide may bedetected by a detection apparatus (e.g., by a CCD camera or othersuitable detection means).

Use of the sequencing method outlined above is a non-limiting example,as essentially any sequencing methodology which relies on successiveincorporation of nucleotides into a polynucleotide chain can be used.Suitable alternative techniques include, for example, pyrosequencingmethods, FISSEQ (fluorescent in situ sequencing), MPSS (massivelyparallel signature sequencing), or sequencing by ligation-based methods.

Example 2: Cell-Free DNA

It is a major challenge to distinguish true variants from backgroundnoise for rare variant discovery. Typically, large amounts of sequencingdata (high sequencing depth) are required to differentiate a truevariant from an amplification and/or sequencing error using previousmethods. In addition, the heterogeneity of mutations within populationsof rare cells in liquid biopsy samples, such as plasma or saliva, makeit difficult to distinguish between sequencing-related errors and truesomatic mutations originating from tumors. Methods and constructsprovided herein do not necessarily require such large sequencing depths,thereby dramatically reducing the costs associated with sequencing.

Studying cell-free DNA (cfDNA) proves to be a useful test case fortesting the capabilities of the linked duplex sequencing methodsdescribed herein, for recovering sequencing depth and for detecting raremutations in a clinical application. Nucleic acids, e.g., cfDNA, arereleased into the bloodstream and other body fluids as part of naturalcell apoptosis, necrosis, and secretion, and comprises both single- anddouble-stranded DNA fragments that are relatively short (overwhelminglyless than 200 base-pairs) and are normally at a low concentration (e.g.1-100 ng/mL in plasma). It is known that the concentration of cfDNA andctDNA in plasma correlates with tumor size and stage. For example,patients having stage I cancer types had fewer than 10 copies per 5 mlof tumor mutations in plasma. In contrast, the copy number increased 10to 100 times among late-stage patients (Hague et al. bioRxiv. 2017;237578). Thus, ctDNA assays used for early cancer diagnosis should behighly sensitive. Commercial solutions require UMIs on both strands ofthe double-stranded template, followed by low-error sequencing. Todetermine a true variant using previous commercial solutions, largeamounts of sequencing data (high sequencing depth) is required togenerate a consensus sequencing read to confidently ascertain a singlenucleotide change.

Recent cancer genome sequencing studies have shown that virtually allcancers harbor somatic genetic alterations. These alterations includeinsertions, deletions, single-base substitutions, and translocations(Vogelstein et al Science. 2013 Mar. 29; 339(6127): 1546-1558). Incancer, a proportion of cfDNA circulating in plasma can come from thetumor, with the relative contribution of cfDNA coming from the tumorincreases with cancer severity. The rate of these chromosomal changes incancer cells is elevated and mutations can be challenging to detectaccurately (Pietrasz et al Clin Cancer Res. 2017 Jan. 1; 23(1):116-123).While typical commercial sequencing instruments have a sequencing errorrate that varies from about 0.05-1% (Quail et al Nat Methods. 2008December; 5(12):1005-10), and can reveal comprehensive genomicalterations, it remains a challenge to distinguish variants at such lowfraction from background errors of sequencing. Nonetheless, identifyingcfDNA harboring these genetic alterations serves as valuable biomarkersand accurately detecting these variants will significantly improvecurrent methods of cancer diagnosis, cancer progression monitoring,therapy effectiveness, and early-stage detection.

To address these issues, we designed a protocol described herein forligating two different adapters at each end of a double strandedtemplate nucleic acid. High accuracy sequencing reads would beparticularly useful for rare variant detection in cfDNA. DNA variantscannot be statistically distinguished from sample prep and/or sequencingerrors when they are present within a sample at a frequency below theerror rate of the sequencing method (typically between 0.05-1%). Bylinking the parent DNA strands together with a hairpin adapter asdescribed herein, and sequencing both strands of the double strandedtemplate nucleic acid, sample prep and sequencing errors can bedistinguished from true variants by identifying discordant base callsbetween the complementary sequencing reads. True genetic variants willbe observed as mutations on both strands, whereas errors will only beobserved as mutations on a single strand. The sequencing methoddescribed herein allows for very high accuracy results by identifyingand correcting for errors within the data which in turn increases thesensitivity for rare variant detection. In general, since twoindependent sequencing measurements are made for the same base, that is,one for each strand, the accuracy of the consensus base call is theproduct of the error rate for each individual base call. For example ifthe single-pass error rate is 10⁻³ (Q30), then pairwise sequencing usingthe methods described allows for a double pass rate to be at leastdouble the single-pass rate, i.e., 10⁻⁶ (Q60).

Blood samples (4-6 ml) are collected from patients into EDTA tubesduring routine phlebotomy. Plasma is separated by centrifugation withFicoll solution at 2,000 rpm for 15 min and transferred intomicro-centrifuge tubes. Then, the plasma is further centrifuged at13,000 rpm for 10 min to remove cell debris. The supernatant is storedat −80° C. before extraction.

The cfDNA is extracted from 1 mL aliquots of plasma using the QIAampcirculating nucleic acid kit (Qiagen). Typically, cfDNA is approximately160-180 bp, and additional fragmentation is not necessary. Depending onthe average sizes of the cfDNA, the cfDNA sample may be optionallyfragmented to an average size of approximately 160-200 bp by enzymaticfragmentation, or other fragmentation/sizing method known in the art.The extracted DNA is then end repaired, dA-tailed using known methods inthe art, and ligated using the two classes of adapters (e.g., S1 and S4sequences comprise the Y adapter as described in Table 1; and the B1,B10, or B14 hairpin adapter as described in Table 2) as described hereinto yield adapter-target-adapter nucleic acids. The resultingadapter-target-adapters may then be amplified and sequenced as describedherein.

An example workflow is provided herein that was used to sequence samplesof cfDNA. Linked-paired strand libraries were prepared in triplicatewith 100 ng of cfDNA (Horizon catalog #HD780) with wild type or a 1%allelic frequency. Pre-fragmented cfDNA was end repaired, dA tailed, andPhosphorylated using the NEBNext® End Repair Module (E6050S) at 20° C.for 30 minutes, 65° C. for 3 minutes followed by bead purification. 0.8uM adapters (S1 (SEQ ID NO:1), S2 (SEQ ID NO:3), and B14 (SEQ ID NO:18)) were then ligated onto the DNA molecules using 16 U/uL T4 DNALigase, 1×T4 DNA Ligase buffer at 25° C. for 15 min followed by a beadpurification step. Next, the B14 hairpin adapter loop region wascaptured to isolate desired constructs containing a hairpin fromunwanted side products (e.g., S1/S2 adapter library contaminants and/oradapter dimers). 5 pmoles of a biotinylated probe was hybridized to thelibrary at 45° C. for 15 minutes. 50 ug of My1C1 streptavidin beads wereincubated with biotinylated probe bound-library molecules in a bufferrotating at room temperature for about 30 minutes. Unbound componentswere washed away using a wash buffer and products were eluted/denaturedoff of capture probe using 0.1 M NaOH and then quenched with 200 mMTris-HCl pH 7.0. The eluent was split into two PCR reactions amplifiedwith 0.5 uM S1, S2 primers (i.e., primers complementary to a portion ofS1 and S2, respectively), 0.5 mM dNTPs, 1×SD polymerase buffer, salts,and 10 Units SD Polymerase. PCR thermocycling was performed (e.g.,cycling parameters included an initial denaturation at greater than 90°C. for at least 1 min, followed by thermally cycling between 95° C.-68°C. followed by maintaining the temperature at about 70-75° C. for about5 minutes. Finally, a bead purification step was performed to isolatethe amplified molecules.

Affinity Capture: 500 ng of linked-paired strand library molecules wereopened up by denaturing, then hybridizing a 5′ phosphorylated primer(one for each hairpin complement) in the hairpin loop and extending witha strand displacing polymerase, 0.5 mM dNTPs, 10 Units SD polymerase,1×SD polymerase buffer, 60 pmoles of each primer. The reaction washeated to 92° C. for about 1 minute followed by cooling to less than 60°C. for about 15 minutes and then purified with bead purification. Anaffinity capture was performed with the XGen Pan-Cancer Panel v1.5 (IDT#1056205) and the protocol was followed per manufacturersrecommendations with a few modifications, such as eliminating the heatstep during hybridization. Hybridization was performed for about 16hours at 65° C. and custom blockers were used that were appropriate forthe adapters. After capture, digestion of the previously extended“blocker” strand is done with Lambda Exonuclease [1×SD buffer, 3 mM Mg,5 Units Lambda Exonuclease] and then PCR amplification and bead sizeselection purification was performed. Clustering: A 4 lane flow cellcontaining immobilized primers (referred to as S1 and S2, havingcomplementarity to S1 (SEQ ID NO:1), S2 (SEQ ID NO:3), or complementsthereof) 28 bp in length was used for clustering. 2 pM ofY-template-hairpin (e.g., having the general structure depicted in FIG.1A) libraries with cfDNA (wild type or 1% allelic frequency) were mixedwith an aqueous solution containing ethylene glycol and a buffer andloaded onto the flow cell which was placed at 85° C. The temperature wasslowly reduced to 45° C. for template seeding. First, extension wasperformed at 60° C. for at least 20 minutes to copy the template ontothe anchored primers, followed by removal of the non-anchored templatestrand with 0.1 M NaOH. The anchored templates were amplified via asolid-phase nucleic acid amplification reaction for 45 cycles (bridgePCR amplification) using a strand displacing polymerase (e.g., Bst largefragment (Bst LF) polymerase, Bst2.0 polymerase, Bsu polymerase, SDpolymerase, Vent exo-polymerase, Phi29 polymerase, or a mutant thereof))0.2 mM dNTPs and a combination of denaturants (e.g., betaine, dimethylsulfoxide (DMSO), ethylene glycol, formamide, glycerol, guanidinethiocyanate, 4-methylmorpholine 4-oxide (NMO), or a mixture thereof).One of anchored strands was cleaved from the surface with enzymes ableto cleave Uracil, thereby leaving the forward or the reverse complementof the construct on the surface. Surface primers and free 3′ ends wereblocked using terminal transferase and dideoxy (ddNTPs) for 30 minutes.A primer complementary to a portion of the hairpin loop was hybridizedand extended using a strand displacing polymerase to free up one arm ofthe construct for sequencing. 1 uM of a sequencing primer complementaryto the 51′ foot region on the construct was hybridized. Sequencing Read1: 105 cycles of sequencing were performed. Preparation of the constructfor Read 2: The extended “blocking” strand was removed with 0.1M NaOH. 1uM of an oligo complementary to a portion of the hairpin loop adapterand a Bgl II restriction site was hybridized and cleaved with Bgl IIrestriction endonuclease. These sequences were removed with NaOH 0.1M. 1uM of a second sequencing primer complementary to the remaining adapterwas hybridized and ready for sequencing. Sequencing Read 2: 155 cyclesof sequencing was performed. Bioinformatically combining the resultsfrom sequencing read 1 and sequencing read 2 results in a consensusread. Since two independent sequencing measurements (i.e., sequencingread 1 and sequencing read 2) are made for the same base, that is, onefor each strand, the accuracy of the consensus base call is the productof the error rate for each individual base call. For the firstsequencing read, the average error rate is 0.01-0.001, that is 10⁻³(Q30). Following the generation of a consensus read, then pairwisesequencing using the methods described allows for a double pass rate tobe double the single-pass rate, i.e., 10⁻⁶ (Q60). In embodiments, theaccuracy is 99.99%. In embodiments, the accuracy is 99.999%. Inembodiments, the accuracy is 99.9999%. In embodiments, the accuracy isbetween about 99.9999% to 100%. In embodiments, the accuracy is betweenabout 99.999% to 100%. In embodiments, the accuracy is between about99.99% to 100%. See for example, the accuracy per sequencing cycle bysequencing the constructs and generating a consensus read according tothe methods described herein in FIG. 20.

Following sequencing of cfDNA and acquiring the resulting reads,overlapping bases for each read pair are identified, and bases where thesequence for the first read (i.e., Read 1) varies from the expectedcorresponding complementary base in the second sequencing read (i.e.,Read 2) are either marked as a no-call (called “N” in sequence) or themost likely base is chosen based on base quality scores. These reads aremapped to a reference genome. The process of mapping identifies thegenomic origin of each fragment on the basis of a sequence comparison.For example, it is possible to determine if a given fragment of cfDNAwas originally part of a specific region of chromosome 18.

The methods described herein are typically in reference to cfDNA and/orctDNA, however they may equally apply, mutatis mutandis, to cfRNA.Technological advances are developing that enable the capture andisolation of cfRNA and ctRNA, see for example Beck, et al. BMC Cancer19, 603 (2019) and Sorber, et al. Cancers, 11(4), 458 (2019), andBenayed et al. Clin Cancer Res. 2019(15):4712-4722, each of which isincorporated herein by reference.

Example 3: FFPE Samples

Formalin fixation and paraffin embedding (FFPE) has been the standardsample preparation method for pathologists, however the quality of thenucleic acid (e.g., DNA or RNA) extracted from FFPE blocks is highlyvariable due to nucleic acid damage introduced by the fixation process.Formalin fixation results in hydrolysis of the phosphodiester bonds,leading to varying degrees of fragmentation. Furthermore, formalin iscapable of interacting (i.e. crosslinking) with cytosine nucleotides oneither strand, which can result in mutations during amplification.

The methods described herein permit sequencing of two distinct regions,one at each end of the complementary strands of a target polynucleotideduplex. Sequencing the complementary original strands of dsDNA would aidin differentiating between true variants and errors due to DNA damagecaused by FFPE storage. The protocol as described in the application,consists of ligating two different classes of adapters at each end of adouble stranded template nucleic acid. Additional protocols and reactionconditions may be found in, for example, Kau and Makrigiorgos NucleicAcids Research, 2003, Vol. 31, No. 6 e26.

Extraction of nucleic acids from FFPE samples is accomplished utilizingcommercial solutions, such as the Nucleic Acid Isolation Kit for FFPE(Cat. No. AM1975) or Invitrogen™ MagMAX™ FFPE DNA Isolation Kit (Cat.No. 4463578). Both procedures perform proteolytic digestions followed bypurification with solid-phase extraction. Typically, FFPE DNA may notrequire additional fragmentation (e.g., badly damaged FFPE DNA), howeverthe sample may optionally be fragmented to an average size ofapproximately 160-200 bp enzymatic fragmentation, or otherfragmentation/sizing method known in the art. The fragments are then endrepaired, dA-tailed using known methods in the art, and ligated usingthe two classes of adapters (e.g., S2 and S5 sequences comprise the Yadapter as described in Table 1; and the B2, B10, or B14 hairpin adapteras described in Table 2) as described herein to yieldadapter-target-adapter nucleic acids. The resultingadapter-target-adapters may then be amplified and sequenced as describedherein.

Example 4: AML Rare Mutation Detection

Typically, the conventional technology for measuring cellular mutationsand heterogeneity for complex diseases includes bulk sequencing, whichprovide average variant allele frequencies. However, using averages toresolve mutational co-occurrences across cell lines is difficult andfurther, relying on averages may miss rare cancer mutations. Movingbeyond averages helps deliver on the promise of precision medicine.

Traditional sequencing paradigms struggle to characterize instances ofAML (acute myeloid leukemia). AML is a cancer of the myeloid line ofblood cells, which results in impaired hematopoiesis and bone marrowfailure. Two or more driver mutations are frequently observed in one ormultiple genes in AML. The most common gene mutation is found in thetumor suppressor and DNA repair gene TP53, however specific mutations ingenes such as FLT3, SF3B1, NPM1, and KIT may influence the outcome ofthe disease. For example, TP53 possesses a c.722 C>G mutation and SF3B1may have a c.2098 A>G mutation. A major challenge has been theunambiguous identification of potentially rare and geneticallyheterogeneous neoplastic cell populations, however using the methodsdescribed herein will address these and other problems known in the art.The sequencing method described herein will allow for very high accuracyresults; for example if the single-pass error rate is 10⁻³ (Q30), thenpairwise sequencing using these methods would allow for a double passrate to be 10′ (Q60).

To do so, a collection of cells (e.g., peripheral blood mononuclearcells (PBMCs) from AML patients and a control population of cells) arelysed and treated using known techniques in the art to extract DNA fromhistones and other DNA-binding proteins. The DNA-lysates may beblunt-ended or polished prior to ligating adapters.

The resulting DNA-lysates are ligated to two different adapters, whereinone adapter is a UMI containing adapter (e.g., a Y adapter as depictedin FIG. 2A, a hairpin adapter in FIG. 2B, or a hairpin adapter shown inFIG. 4) wherein the UMI is used to uniquely identify the origin of theDNA. The resulting adapter-target-adapters are then amplified (e.g., asdepicted in FIG. 8) and sequenced as described herein. Followingsequencing and acquiring the resulting reads, these reads are mapped toa control genome permitting the detection of gene mutations.

Example 5: Selective Sequencing

For some samples, only a subset of polynucleotides in a sample arerelevant to a particular assay. In such cases, it can be faster, moreefficient, and even more sensitive to sequence only that subset.Selectively enriching a population of polynucleotides by probehybridization is simpler when the target polynucleotides are linear, asthe strands can be denatured from one another by distances that allowfor easier competition with probe oligonucleotides. However, when twostrands of a target polynucleotide are joined by one or more loops(e.g., when ligated to a hairpin adapter on one or both ends), the twostrands remain in close proximity when denatured, and more easilyre-hybridize with one another. This ease of re-hybridization increasescompetition with probe oligonucleotides for binding their respectivetarget sequence and can decrease recovery of target sequences. Examplemethods for displacing a strand of a target polynucleotide ligated to atleast one hairpin adapter to increase probe capture efficiency areprovided herein.

A first method is the use of one or more biotinylated single strandedprobe oligonucleotides, or “biotinylated capture probes”, which areannealed to specific regions of polynucleotide duplexes comprising adouble stranded nucleic acid of interest annealed to a Y-adapter and ahairpin adapter, therefore labeling said polynucleotide duplexes. Inthis method, an initial step of denaturation (i.e. strand dissociation)is used to allow the biotinylated probes, to bind to the first strandand/or second strand of the target nucleic acid. The resultingbiotin-labeled complexes can then be purified via methods ofpurifications based on avidin, streptavidin, or neutravidin, or can becaptured via the available regions of the previously double strandedtemplate nucleic acid, now single stranded. FIG. 9 presents an exampleof such a method of labeling a polynucleotide duplex of interest, viathe use of a biotinylated probe complementary to a region of the firststrand of the polynucleotide duplex (the template nucleic acid), a stepof heat induced denaturation at 95° C., and a following step ofannealing of the probe to its target region in the first strand of thetemplate nucleic acid, therefore labeling it.

Another method is the use of modified nucleotides in the hairpin loop ofa polynucleotide duplex including a double-stranded nucleic acid ofinterest ligated to a Y-adapter and a hairpin adapter. In this method,the modified nucleotides are selected to create a “temporary stop,”which stops polymerase extension of a primer complementary to thesingle-stranded 3′ end of the Y-adapter. The result of this method isthe formation of a double-stranded product, in which the second strandof the polynucleotide duplex is single-stranded and available forcapture (e.g. by a surface-bound primer, complementary to a specificregion of the second strand of the polynucleotide duplex). Followingcapture, the temporary stopper can be removed. FIG. 10 presents anexample of such method.

In one example implementation of a temporary stopper, a polymerase(e.g., phi-29) can be used to extend a primer complementary to thesingle stranded 3′ end of the Y-adapter, up to the temporary stoppercontaining one or more modified nucleotides. After capture of thepolynucleotide duplex, another enzyme that is capable of extending theproduct of the first polymerase beyond the temporary stopper (e.g. Pfu)can be used for subsequent steps. In another example implementation, thetemporary stopper is composed of one or more modified nucleotides with acleavable linker (e.g., 5′, 3′, or a base) containing PEG, therebyblocking the extension of a primer complementary to the single stranded3′ end of the Y-adapter, up to the temporary stopper. After capture ofthe polynucleotide duplex, the linker(s) can be cleaved so as to removethe PEG. In another example implementation, the temporary stopper iscomposed of one or more modified nucleotides linked to biotin, to whicha protein (e.g., streptavidin) can be bound, thereby blocking polymeraseextension. After capture of the polynucleotide duplex, the reactionconditions can be modified (e.g., increased salt concentration, and/or,increased temperature) so as to release the protein, or proteins, boundto the one or more modified nucleotides. In another exampleimplementation, the temporary stopper is a modified nucleotide, such asiso dGTP or iso dCTP, which are complementary to each other. In areaction of polymerization lacking the complementary modifiednucleotides, the extension of a primer complementary to thesingle-stranded 3′ end of the Y-adapter is therefore only possible up tothe temporary stopper. After capture of the polynucleotide duplex, thecorresponding complementary modified nucleotide (iso dGTP in the case ofiso dCTP in the loop) can be added to the solution, therefore allowingthe polymerization process to proceed. In another exampleimplementation, the temporary stopper comprises one or more sequenceswhich is recognized and bound by one or more single-stranded DNA-bindingproteins, thereby blocking polymerase extension at the bound site. Aftercapture of the polynucleotide duplex, the reaction conditions can bemodified (e.g., increased salt concentration, and/or, increasedtemperature) so as to release the protein(s), therefore allowingpolymerization to proceed. In another example implementation, thetemporary stopper comprises one or more sequences which are recognizedand bound by one or more short RNA or PNA oligos, thereby blocking theextension by a strand displacing DNA polymerase that cannot stranddisplace RNA or PNA. For example, after capture of the polynucleotideduplex, RNase H can be then used to digest the RNA oligos, thereforeallowing the polymerization process to proceed. In embodiments, aftercapture of the polynucleotide duplex, the PNA is subjected to denaturingconditions (e.g., increasing the temperature to release the PNA); RNaseH can be then used to digest the oligos, therefore allowing thepolymerization process to proceed.

Another method is the use of a primer complementary to the hairpin loopor stem of a hairpin adapter, within a polynucleotide duplex including adouble stranded nucleic acid of interest ligated to a Y-adapter and thehairpin adapter. In this method, a primer hybridizes to a complementaryregion within the hairpin loop, and a strand-displacing enzyme extendsfrom the primer to form a double-stranded product. With the formation ofa double-stranded product, the first strand is single stranded andavailable for capture (e.g., a surface-bound complementaryoligonucleotide). FIG. 11 presents an example of such method.

Another method is the use of an insertion primer complementary to aportion of the 5′ region of the double stranded portion of a hairpinadapter (an “invasion primer”), within a polynucleotide duplex includinga double stranded nucleic acid of interest ligated to a Y-adapter andthe hairpin adapter. In this method, a recombinase (e.g., T4 UvsXprotein), assisted by a loading factor (e.g., T4 UvsY), and theinsertion primer, form a nucleoprotein complex, wherein the insertionprimer hybridizes to a complementary region of double stranded DNA.Additional cofactors (e.g., single-strand binding protein, ATP, salts,etc.) may also be used to facilitate hybridization. The complex invadesthe double stranded DNA target region and a strand exchange occurs,forming a D-loop. Once the D-loop forms, the recombinase complexdissociates. A strand-displacing DNA polymerase extends to form adouble-stranded product. With the formation of a double-strandedproduct, the first strand is single stranded and available for capture(e.g., hybridizing to a surface-bound complementary oligonucleotide).FIG. 12 presents an example of such method.

Another method is the use of an insertion primer complementary to aportion of the 5′ region of the double stranded portion of a hairpinadapter or Y-adapter within a polynucleotide duplex including a doublestranded nucleic acid of interest ligated to a Y-adapter and the hairpinadapter. In embodiments, the method includes generating a blockingstrand. In embodiments, generating the blocking strand includes aplurality of extension cycles. In embodiments, generating the blockingstrand includes extending the primer by incorporating one or morenucleotides (e.g., dNTPs) using Bst large fragment (Bst LF) polymerase,Bst2.0 polymerase, Bsu polymerase, SD polymerase, Vent exo-polymerase,Phi29 polymerase, or a mutant thereof. With the formation of adouble-stranded product, the first strand is single stranded andavailable for capture (e.g., hybridizing to a surface-boundcomplementary oligonucleotide) or sequencing.

Another method is the use of a biotinylated insertion probe (e.g., abiotinylated invasion capture probe) complementary to any region of apolynucleotide duplex including a double stranded nucleic acid ofinterest ligated to a Y-adapter and a hairpin adapter. In this method, arecombinase (e.g., T4 UvsX protein), assisted by a loading factor (e.g.,T4 UvsY), and an invasion capture probe complementary to a target regionof a polynucleotide duplex, form a nucleoprotein complex, wherein theinsertion primer hybridizes to the complementary region of doublestranded DNA of the polynucleotide duplex. Additional cofactors (e.g.,single-strand binding protein, ATP, salts, etc.) may be used tofacilitate hybridization. The complex invades the double stranded DNAtarget region and a strand exchange occurs, forming a D-loop. Once theD-loop forms, the recombinase complex may be dissociated. Thebiotinylated capture probe is therefore then bound to the targetsequence, and this biotinylated complex can be pulled down and purified.FIG. 13 presents an example of such method, wherein the biotinylatedinvasion capture probe is complementary to a region of the second strandof the template nucleic acid of a polynucleotide duplex, including thetemplate nucleic acid of interest ligated to a Y-adapter and a hairpinadapter.

Example 6: De Novo Assembly of Bacterial Genomes

Microbial genome sequencing has revealed how microorganisms adapt,evolve, and contribute to health and disease. With respect to bacterialgenomes, the de novo assembly of short reads (100-300 bp) can result infragmented assemblies, particularly because of the widespread presenceof repetitive sequences. These repetitive sequences are often longerthan the length of a short read and the span of paired-end reads. Forexample, antimicrobial resistance regions are often flanked byrepetitive insertion sequences; in such a case, from an incompleteshort-read assembly, it would be impossible to determine whetherresistance regions are present in chromosomes or plasmids (Liao Y C etal. Front. Microbiol. 2019; 10:2068). As such, faithful de novo assemblyof bacterial genomes typically requires larger inserts, for example, 1kbp or larger.

Existing methods for de novo bacterial genome assembly include the useof long-read sequencing technology such as that of Pacific Biosciencesand Oxford Nanopore, both of which report higher error rates and lowerthroughput in comparison to other sequencing methods (e.g.,sequencing-by-synthesis technologies). Alternatively, large-scale genomeassembly can use mate pair sequencing to generate long-insert paired-endDNA libraries, however the relatively laborious and lengthy protocolthat generates long insert sizes needed for mate pair sequencingtypically produces a large proportion of duplicates and chimericvariants that reduces true coverage and insight. Still, a majorchallenge is the higher rate of sequencing errors abundant in theseexisting methods, in combination with base composition bias and thecomplexity of repetitive regions in genomes, leading to complicated andunsatisfactory sequence assembly (Liao X et al. Quant. Biol. 2019;7(2):90-109). The methods described herein address these and otherproblems. For example, the compositions and sequencing methods describedherein will allow for high-accuracy pairwise sequencing of large-insert(e.g., 500-1500 bp) genomic libraries.

Bacterial genomic DNA is purified from isolated cultures using acommercial solution, such as the NEB Monarch® Genomic DNA PurificationKit (Cat. No. T30105). The extracted genomic DNA is fragmented to anaverage size of approximately 1000 bp by enzymatic fragmentation, orother fragmentation/sizing method known in the art. The fragments arethen end repaired, dA-tailed using known methods in the art, and ligatedusing the two classes of adapters (e.g., S2 and S5 sequences comprisethe Y adapter as described in Table 1; and the B2, B10, or B14 hairpinadapter as described in Table 2) as described herein to yieldadapter-target-adapter nucleic acids. The resultingadapter-target-adapters are amplified and sequenced as described herein.Following sequencing and acquiring the resulting reads, these reads arethen assembled using bioinformatic tools known in the art to generatethe complete bacterial genome. These methods could also be applied toother prokaryotic and eukaryotic de novo genome assembly efforts.

Example 7: Alternative Splicing Analysis

Alternative splicing (AS) is a key post-transcriptional regulatorymechanism in which alternative splice sites are selected to generatemore than one transcript from heterogenous nuclear RNA (hnRNA)transcripts (Wahl MC Cell 2009; 136:701-718). During AS, intronicsequences are defined by the dinucleotide conserved sequence motifs atthe intron/exon junctions, usually GT-AG, which are respectively namedas 5′ donor site and 3′ acceptor site. Other intron/exon junctiondinucleotide sequence motifs have also been reported, including AT-AC,GC-AG, and GT-GG (Dubrovina A S et al. Biomed. Res. Int. 2013).Different transcript isoforms may encode proteins with differentfunctions or affect the mRNA stability of translational capacity. Formultiexon mRNA, the splicing mode may vary in multiple ways, includingintron retention, exon skipping, and alternative donor/acceptor sites,dramatically increasing the complexity of the entire transcriptome andproteome (Li Y et al. The Plant J. 2016; 90(1):164-176).

Accurate detection of AS events remains a challenge due to thelimitations of short-read sequences in reconstructing full-lengthisoforms (Hu H et al. Front. Genet. 2020; 11:48). These disadvantagesgenerally lead to gene prediction without reliable annotation onalternative isoforms and untranslated regions, which can limit their useto characterize the post-transcriptional processes. Therefore, theidentification of full-length splice isoforms is essential for a deepunderstanding of the transcriptome complexity and its potential role ingene regulation. Much like de novo bacterial genome assembly (seeExample 6), AS detection will benefit from a longer insert size andreliable capture of AS-related motifs. A comparison between PacBio'sSMRT sequencing and Illumina's RNA-seq platforms (Li Y et al. The PlantJ. 2016; 90(1):164-176) indicated that SMRT, which utilizes longerread-length technology, was able to identify more genes undergoing ASthan standard RNA-seq, although still lacked reliable capture of allknown AS events. The sequencing method described herein allows forhigh-accuracy pairwise RNA sequencing of a large-insert library toenable efficient AS site detection.

Briefly, total RNA is extracted from a sample for AS analysis using acommercial solution such as the RNeasy Mini Kit (Qiagen). Ribosomal RNA(rRNA) is then depleted using a commercial solution such as the NEBNext®rRNA Depletion Kit V2 (Cat. No. E7405S). While polyA+ selection istypically used for RNA-seq protocols, rRNA depletion has been shown tocapture significantly more transcriptome features useful for AS analysis(see, for example, Zhao S et al. Scientific Reports 2018; 8: 4781). TheRNA is then fragmented to an average size of greater than 200 bases, forexample, approximately 200-300 bases, or approximately 300-400 bases, orapproximately 400-500 bases, or approximately 500-600 bases, orapproximately 600-700 bases, or approximately 700-800 bases, usingstandard methods for RNA fragmentation such as acoustic shearing orincubation with divalent cations, e.g. Mg²⁺, at elevated temperatures.

The fragmented RNA is then reverse transcribed and converted todouble-stranded cDNA using commercial solutions, for example, theInvitrogen™ SuperScript™ Double-Stranded cDNA Synthesis Kit (Cat. No.11917010). The cDNA is then dA-tailed using known methods in the art,and ligated using the two classes of adapters (e.g., S1 and S4 sequencescomprise the Y adapter as described in Table 1; and the B1, B10, or B14hairpin adapter as described in Table 2) as described herein to yieldadapter-target-adapter nucleic acids. The resultingadapter-target-adapters may then be amplified and sequenced as describedherein.

Following sequencing of cDNA and acquiring the resulting reads, theidentification of major AS events, including exon skipping events,intron retention, alternative 5′ donor, and alternative 3′ donor usagecan be accomplished through bioinformatic analysis, including the use ofpublicly available tools such as JUM (Wang Q and Rio DC Proc. Natl.Acad. Sci. 2018; 115(35):E8181-E8190) and PASA (Campbell M A et al. BMCGenomics 2006; 7:327). Identified AS events can then be cross-checkedwith known AS databases and reference genomes.

Example 8: Sequential Ligation on a Solid Support

An alternative schematic showing the process for asymmetrical adapterligation is shown in FIGS. 14A-14C. Depicted in FIG. 14A (right side),the target DNA is double stranded and contains a 5′ phosphate forligation. Embodiments of the hairpin adapters are described throughoutthe specification, for example in FIG. 4 and FIG. 5. The loop of thehairpin adapter includes a priming region (PR), depicted in FIG. 14 asP3. The loop of the hairpin adapter may include an optional UMI (uniquemolecular identifier; barcode).

To circularize the ds template DNA, a first hairpin adapter ishybridized to a surface-immobilized oligo, referred to as P3′ in FIGS.14A-14B. Generally, to form a cluster of monoclonal amplicons aplurality of immobilized oligos are present on the surface, however forclarity only one oligo is shown. After the first hairpin adapter ishybridized and excess unhybridized hairpin adapter are removed, thedsDNA is introduced and ligated to the first hairpin adapter to formadapter-duplex (see FIG. 14A). After ligation, any excess dsDNA isremoved. A second hairpin adapter is introduced and ligated to theadapter-duplex to form a circularized product, wherein the secondhairpin adapter includes a different PR (i.e., P1 and P2 as illustrated)than the first hairpin adapter (see FIG. 14B). The circularized productmay then be subjected to circular amplification methods (e.g., RCA oreRCA) to produce a long continuous single stranded product.Alternatively, as shown in FIG. 14C a Y-adapter is introduced, depictedas P1 and P2 in FIG. 14C, and ligated to the adapter-duplex to form anadapter-target-adapter construct resembling a bobby-pin structure.

Surface-conjugation of oligos to flow cell: A plurality of primers,referred to as P3′, are chemically attached to a polymer-coated glassslide through a linker via DBCO-azide click chemistry. Thispolymer-coated glass slide is assembled into a flow cell prior to primerdeposition.

Hybridization of hairpin adapter 1 to surface primer: A hairpin adapterwhich contains a 5′ phosphate, a 13 nt stem region (a stem region whichis stable below 45° C.) and a loop sequence which is complementary tothe P3′ surface primer is hybridized to the flow cell at 37° C. for 30minutes in a DNA hybridization buffer. After hybridization, excessunhybridized hairpin adapter is washed out of the flow cell.

Ligation of Target Sequence: A target sequence (e.g., dsDNA) which hasbeen fragmented, polished, and 5′ phosphorylated is introduced to theflow cell in a mixture of buffer and T4 DNA ligase and then incubated at25-37° C. for 1-3 hours for ligation of target sequence onto adapter 1.After ligation, any excess target sequence is washed out of the flowcell.

Ligation of Adapter 2 onto Target Sequence: A second hairpin adapterwhich contains a 5′ phosphate, a 13 nt stem region (stable below 45° C.)and a loop sequence which contains the P1 sequence and P2 sequence isintroduced to the flow cell in a mixture of buffer and T4 DNA ligase andthen can be incubated at 25-37° C. for 1-3 hours for ligation of adapter2 onto target sequence. Alternatively, a Y-shaped adapter is introducedto the flow cell in a mixture of buffer and T4 DNA ligase and then canbe incubated at 25-37° C. for 1-3 hours for ligation of adapter 2 ontothe target sequence. After ligation, excess adapter is washed out of theflow cell. The adapter-target-adapter constructs are then amplifiedaccording to the methods described herein to form monoclonal clusters ofamplicons. The resulting clusters can be visualized by staining theamplified product with SYBR-Gold and visualized using fluorescentmicroscopy.

Example 9: Linked Duplex Methylation Profiling

Somatic mutations alone may not provide adequate information about thetumor site. Epigenetic information, such as biomolecule methylation,and/or additional protein biomarkers combined with cfDNA and ctDNAanalyses is useful in determining the tumor origin at an early stage.Biomolecule methylation, such as DNA methylation, is widespread andplays a critical role in the regulation of gene expression indevelopment, differentiation, and disease. Methylation is an epigeneticmodification in which a methyl group is added to cytosines and/oradenine nucleobases, and frequently occurs in regions of DNA where acytosine nucleotide is followed by a guanine nucleotide in the linearsequence of bases along its 5′→3′ direction, referred to as a CG or CpGsite. In particular regions of genes, for example gene promoter regions,an increase in cytosine methylation at gene promotor regions can inhibitthe expression of these genes (Robertson K D Nat. Rev. Genet. 6, 597-610(2005)). The gene silencing effect of methylated regions is accomplishedthrough the interaction of methylcytosine binding proteins with otherstructural components of the chromatin, which, in turn, makes the DNAinaccessible to transcription factors through histone deacetylation andchromatin structure changes (Greenberg MVC and Bourc'his D Nat. Rev.Mol. Cell Biol. 20, 590-607 (2019)). Cancers take advantage of thismechanism, and hypermethylate genomic regions associated with DNA repairgenes.

Methylation patterns also play an important role in genomic imprinting,in which imprinted genes are preferentially expressed from either thematernal or paternal allele. Patterns of methylation in a genome areheritable because of the semi-conservative nature of DNA replication.During this process, the daughter strand, newly replicated on amethylated template strand is not initially methylated, but the templatestrand directs methyltransferase enzymes to fully methylate bothstrands. Deregulation of imprinting has been implicated in severaldevelopmental disorders. Moreover, there is abundant evidence thataberrant DNA methylation can preclude normal development.

There are around 25,000 CpG islands in the human genome. CpG islands areusually understood as polynucleotide regions with a length greater than200 bp having GC content greater than 50%. In various cancers such asleukemia, it has been previously reported that there is a globaldecrease in DNA methylation and an increase in methylation specificallyat CpG islands. It is believed that in a normal cell, the CpG islandsare unmethylated and when the cell becomes a tumor cell the CpG islandbecomes methylated at every CpG. It is suspected that in a normal cellthe CpG islands, which are typically located near the promoters ofgenes, are normally kept hypomethylated. In an unmethylated state,cytosine is converted to uracil after deamination, which is recognizedby the cell's repair machinery and is removed, while in a methylatedstate deamination of cytosine results in the formation of thymine whichis not recognized by the repair machinery. Therefore, the presence orabsence of hypermethylation at these CpG islands can be used to detecttumor cells. As cancer cells are constantly evolving to avoid treatmentregimens, there is a need for a method to detect a tumor cell with highaccuracy.

A common method of determining the methylation level and/or pattern ofDNA requires methylation status-dependent conversion of cytosine inorder to distinguish between methylated and non-methylated CpGdinucleotide sequences. For example, methylation of CpG dinucleotidesequences can be measured by employing cytosine conversion-basedtechnologies, which rely on methylation status-dependent chemicalmodification of CpG sequences within isolated genomic DNA, or fragmentsthereof, followed by DNA sequence analysis. Chemical reagents that canbe used to distinguish between methylated and non-methylated CpGdinucleotide sequences include for example, hydrazine, which cleaves thenucleic acid, and bisulfite treatment. Bisulfite treatment followed byalkaline hydrolysis specifically converts non-methylated cytosine touracil, leaving 5-methylcytosine unmodified as described by Olek A.,Nucleic Acids Res. 24:5064-6, (1996) or Frommer et al., Proc. Natl.Acad. Sci. USA 89:1827-1831 (1992), each of which is incorporated hereinby reference in its entirety. The bisulfite-treated DNA can subsequentlybe analyzed by conventional molecular techniques, such as PCRamplification, sequencing, and detection comprising oligonucleotidehybridization.

One consequence of bisulfite-mediated deamination of cytosine is thatthe bisulfite treated cytosine is converted to uracil, which reduces thecomplexity of the genome. Specifically, a typical 4-base genome(A,T,C,G) is essentially reduced to a 3-base genome (A,T,G) becauseuracil is read as thymine during downstream analysis techniques such asPCR and sequencing reactions. Thus, the only cytosines present are thosethat were methylated prior to bisulfite conversion. Because thecomplexity of the genome is reduced, standard methods for comparingand/or aligning a bisulfite-converted sequence to the pre-conversiongenome can be cumbersome and, in some cases, ineffective. For example,problems may arise when aligning converted fragments to the genome,especially when using short sequences. Accordingly, there remains a needfor methods which facilitate identification of the genomic context ofbisulfite converted DNA.

Provided herein are methods and compositions that relate to sequencingnucleic acids and determining the methylation level and/or pattern ofthe nucleic acids. Using methods and/or compositions described herein,the complexity of the target nucleic acids is preserved by keeping trackof complementary strands after the strands have been subjected tobisulfite conversion of nucleic acids. In order to preserve complexityof the nucleic acid, embodiments of the present invention relate to apairing of the cytosine-converted sequences of both strands of adouble-stranded nucleic acid and using the sequence information fromboth strands to determine the sequence and/or methylation status of oneor both strands prior to conversion.

Linked Duplex Sequencing: Methylated/Unmethylated Cytosine Conversion

Methylation of CpG dinucleotide sequences can be measured by employingcytosine conversion-based technologies. The term “conversion” or“converted” as used herein in reference to 5-methylcytosine and5-hydroxymethylcytosine means the conversion of an unmethylated cytosineto another nucleotide which will distinguish the unmethylated from themethylated cytosine. Typically, the agent modifies unmethylated cytosineto uracil. A commonly used agent for modifying unmethylated cytosinepreferentially to methylated cytosine is sodium bisulfite. However,other agents that similarly modify unmethylated cytosine, but notmethylated cytosine, can also be used in the method of the invention.Sodium bisulfite (NaHSO₃) reacts readily with the 5,6-double bond ofcytosine, but poorly with methylated cytosine, as described by Olek A.,Nucleic Acids Res. 24:5064-6, 1996 or Frommer et al., Proc. Natl. Acad.Sci. USA 89:1827-1831 (1992), each of which is incorporated herein byreference. Cytosine reacts with the bisulfite ion to form a sulfonatedcytosine reaction intermediate which is susceptible to deamination,giving rise to a sulfonated uracil. The sulfonate group can be removedunder alkaline conditions, resulting in the formation of uracil. Uracilis recognized as a thymine by Taq polymerase and other polymerases andtherefore upon PCR or during a sequencing reaction, the resultantproduct contains cytosine only at the position where 5-methylcytosineoccurs in the starting template nucleic acid. Alternatively, conversionmay be accomplished using restriction enzymes, such as HpaII and MspI,which recognize the sequence CCGG.

Traditionally, the recovery of bisulfite-converted DNA is very poor dueto DNA degradation caused by extended-duration sodium bisulfitetreatment protocols and subsequent depyrimidation (Grunau C et al.Nucleic Acids Res. 2001, 29(13):E65-5). Optimized bisulfite conversionprotocols that include a fast deamination step reduce incubation timesfrom 12 to 16 hours to 40 min by using a highly concentrated bisulfitesolution at high temperatures, leading to a more homogenous conversionof cytosine due to the easier process of DNA denaturation at hightemperatures and reduced degradation due to shorter incubation times(Shiraishi M and Hayatsu H. DNA Res. 2004, 11(6):409-15). One study hasshown that bisulfite treatment of cfDNA for 30 min at 70° C. leads tocomplete conversion of cytosine to uracil and is achieved with highpost-treatment DNA recovery (Yi S et al. BMC Molecular Biol. 2017,18:24, which is incorporated herein by reference). Such rapid-bisulfiteconversion can also be used in the method described herein. For example,10 M (NH4) HSO₃—NaHSO₃ bisulfite solution was added toY-template-hairpin constructs. The mixtures are heated for 30 min at 70°C. or for 10 min at 90° C. and subsequently cooled to 4° C.

While bisulfite conversion is the current standard for performing DNAmethylation analysis, it has several drawbacks. As discussed supra,bisulfite treatment is a harsh chemical reaction which can lead to DNAdegradation, severely limiting its utility if sample DNA quantities arelow, as is often the case with cfDNA. Additionally, the completeconversion of unmodified cytosine to thymine reduces sequencingcomplexity, potentially leading to poor sequencing quality, low mappingrates, and uneven genome coverage. A method for bisulfite-free directdetection of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC)has been described (Liu Y et al. Nat. Biotechnol. 2019, 37(4)424-429,which is incorporated herein by reference), which combines ten-eleventranslocation (TET) oxidation of 5mC and 5hmC to 5-carboxylcytosine(5caC) with pyridine borane reduction of 5caC to dihydrouracil (DHU).Subsequent PCR converts DHU to thymine, enabling a C-to-T transition of5mC and 5hmC. This TET-assisted pyridine borane sequencing (TAPS) methodresults in higher mapping rates and more even coverage than bisulfiteconversion and may be applied to the methods described herein for linkedduplex methylation profiling. Another bisulfite-free approach formethylation analysis is the NEBNext® Enzymatic Methyl-seq product, whichfirst protects 5mC and 5hmC from deamination by TET2 and an oxidationenhancer, followed by APOBEC deamination of unprotected cytosines touracils.

Converted DNA can subsequently be analyzed by conventional moleculartechniques, such as PCR amplification, sequencing, and detectioncomprising oligonucleotide hybridization. As described below, a varietyof techniques are available for sequence-specific analysis (e.g., MSP)of the methylation status of one or more CpG dinucleotides in aparticular region of interest. Methods provided herein are particularlyuseful for creating a reference complimentary copy of the pre-conversionsequence for each of a multitude of genomic fragments. Using thesemethods, the reference copy may be covalently linked to the convertedtemplate. By linking parent strands together using the constructsdescribed herein (e.g., the hairpin adapter depicted in FIG. 4), thesequence can be corrected prior to mapping using the second strand,increasing the fraction of properly mapped reads. Additionally, C to Tmutations (SNVs) are distinguishable from converted bases as the “T”mutation will be confirmed by an “A” on the opposite strand enablingboth detection of sequencing variants and methylation state in the sameassay.

The DNA is fragmented, repaired, and adapters ligated as described inExample 1. As a result of cytosine conversion, unmethylated cytosines inthe template nucleic acid are converted to uracil residues, whilemethylated cytosines are unchanged (see, for example, FIG. 15A). Inembodiments, the cytosine-converted construct may be amplified prior tohybridization to increase the amount of material available for clusteramplification, resulting in conversion of the uracil nucleotides (dUTP)to thymine nucleotides (dTTP). In embodiments where the adapteroligonucleotides include a sequence that will be used in later steps(i.e., for capture on a support or for binding of a sequencing primer),the adapter can be synthesized, for example, using a bisulfite-resistantcytosine analog such as 5-methyl dCTP (Me-C, or 5mC) in the positionswhere maintaining a cytosine at that position is important.Alternatively, a hairpin adapter could be ligated to one side of alinear template, with the hairpin adapter functioning as a primer tofill in the second strand of the template with dNTPs including Me-C.Following cytosine conversion, the second strand remains unconverted dueto the incorporated Me-C bases and can serve as a reference for theoriginal converted template strand.

Described herein, the methods use the physical pairing of thecomplementary strands to identify DNA fragments having an asymmetricmethylcytosine profile (e.g., hemimethylated DNA fragments). These canarise from imprinting, but also as a consequence of active demethylationcatalyzed by TET family enzymes (Erlich et al 2012, Shen et al 2014,Song et al 2017), which are misregulated in some cancers. During TETmediated active demethylation, the standard methyl cytosine is convertedto 5-hydroxymethylcytosine as well as additional intermediates, finallyresulting in an unmethylated cytosine. 5-hydroxymethylcytosine and otherintermediates are relatively short lived and are found at low frequencyin a cell type undergoing active demethylation.

Quantifying 5-hydroxymethylcytosine and these additional intermediatesas a liquid biopsy biomarker is helpful at obtaining an epigeneticsnapshot of the cancer status. The methyl moiety of methylated cytosinescan be lost or eliminated e.g., passively during DNA replication, oractively through enzymatic DNA demethylation. During active DNAdemethylation, 5mC is oxidized to produce 5-hydroxymethylcytosine(5hmC), which acts not only as an intermediate during 5mC demethylation,but also plays important roles in many cellular and developmentalprocesses, including the pluripotency of embryonic stem cells, neurondevelopment, and tumorigenesis in mammals. Methods described herein areuseful at quantifying 5mC and 5hmC in both strands of a sample and areuseful at revealing the extent of methylation symmetry in adouble-stranded nucleic acid. For example, using the methods describedherein, one method to detect asymmetric methylation profiles consists of(1) ligating a first adapter and a second adapter to a cfDNA sample,wherein the second adapter is a hairpin adapter, wherein some or all ofthe adapter cytosines of the hairpin adapters are methylated; (2)optionally, capturing fragments using a hybrid capture panel; (3)converting the cytosines (e.g., contacting the sample with bisulfite totreat the fragments, or using an enzymatic conversion methodology); (4)amplifying the converted sample; and (5) sequencing to identify forwardand reverse read mismatches indicative of asymmetric methylation (FIG.16). One useful embodiment of the above approach employs hairpinadapters designed to contain a region consisting of partially methylatedcytosines (e.g., during hairpin oligomer synthesis, request that a givenposition consist of an equal proportion of cytosines andmethylcytosines). Bisulfite conversion provides information on themethylation state of individual cytosines by converting cytosine (butnot 5-methylcytosine) to uracil, and subsequently to thymine upon PCRamplification. Following bisulfite treatment, a subset of the adaptercytosines would undergo conversion and be read as thymine. The resultantrandom 2-base code gives rise to a low complexity “methylcytosine UMI”(FIG. 17A-17B) for use in downstream error correction. Hairpin adapterscould be further improved, in some embodiments, by inclusion of a“bisulfite conversion control region” consisting of one or moreunmethylated cytosines, which undergo bisulfite conversion and are readas thymines. Quantifying the fraction of unconverted cytosines bases inthis region provides an indication of the efficiency of bisulfiteconversion and may serve as a quality control metric.

Linked Duplex Sequencing: Clustering Amplification

Once formed, the library of adapter-target-adapter templates preparedaccording to the methods described above can be used for solid-phasenucleic acid amplification. In some embodiments of the invention, thetemplates used for solid-phase nucleic acid amplification have beentreated with bisulfite to convert any unmethylated cytosines to uracilsusing protocols known in the art. In other embodiments of the invention,the templates used for solid-phase nucleic acid amplification weresubjected to TET oxidation of 5mC and 5hmC to 5caC with pyridine boranereduction of 5caC to DHU, as described supra.

Thus, in another aspect is provided a method of nucleic acidamplification of template polynucleotide molecules which includespreparing a library of template polynucleotide molecules (e.g.,adapter-target-adapter templates) and performing an amplificationreaction (e.g., a solid-phase nucleic acid amplification reaction)wherein the template polynucleotide molecules are amplified. Inembodiments, the method includes providing a plurality of primers (e.g.,P1 and P2) that are immobilized on a solid substrate. Note, however, forclarity only a few immobilized primers are depicted in FIG. 15B.

An adapter-target-adapter construct (i.e., the denatured single strand,reading from 5′ to 3′ having the formula P1-template-P3-template-P2′generated according to methods described herein) is hybridized to acomplementary primer (e.g., the complement to P2′, referred to as P2)that is immobilized on a solid substrate. In the presence of apolymerase (wherein the polymerase is not shown in FIG. 15B) the P2strand is extended to generate a complimentary copy, wherein thedenatured single strand, reading from the 5′ to the 3′ has the formulaP2-template-P3′-template-P1′. The original adapter-target-adapter may beremoved. As shown on the right side of FIG. 15B, the complementarystrand of the converted template will contain adenines that aremispaired with cytosines facilitating identification of methylationsites during sequencing analysis. Because of the self-folding of theadapter-target-adapter construct, initially seeding on the solid surfacecould be done without additional denaturation steps (e.g., as long asthe products are in the hairpin state). In some embodiments, anamplified, cytosine-converted Y-template-hairpin construct hybridizes toan immobilized P2 primer (FIG. 15D), wherein the uracil is replaced witha thymine prior to hybridization. In the presence of a polymerase, acopy of the original template is made; this copy then hybridizes to animmobilized P1 primer as shown in FIG. 15C.

Next, the complimentary copy is annealed to a P1 primer that isimmobilized on the solid substrate, which in the presence of a DNApolymerase (the polymerase is not shown in FIG. 15C) extends P1 primerto reform the original adapter-target-adapter construct (i.e., thedenatured single strand having the formula P1-template-P3-template-P2′)which then hybridizes with an immobilized P2 primer. The products of theextension reaction (i.e., the P1-template-P3-template-P2′ hybridized toan immobilized P2, and P1′-template-P3′-template-P2 hybridized to P1)may be subjected to standard denaturing conditions in order to separatethe extension products from strands of the adapter-target constructs.The adapter-target-adapter constructs may then anneal to a complementaryimmobilized primer and may be extended in the presence of a polymerase.These steps, depicted in FIGS. 15B-15C, may be repeated one or moretimes, through rounds of primer annealing, extension and denaturation,in order to form multiple copies of the same extension productscontaining adapter-target-adapter constructs, or the complementsthereof. The A/C and T/G mismatches are carried forward through eachround of amplification (not shown for clarity on far-right panel of FIG.15C). Note, this bridging amplification is typically more efficient thanamplifying linear strands, because the adapter-target-adapter productsself-fold, thus leaving the primer site accessible.

Sequencing can be carried out using any suitable sequencing-by-synthesistechnique, wherein nucleotides are added successively to a free 3′hydroxyl group, resulting in synthesis of a polynucleotide chain in the5′ to 3′ direction. In embodiments, the identity of the nucleotide addedis determined after each nucleotide addition. In embodiments, detectionof a methylated cytosine is determined by the presence of a G-T mismatchfollowing sequencing of the amplified converted template nucleic acid.Using the methods described herein, SNPs are distinguishable fromconverted G-T base pairs.

Example 10: Differentiating True Variants from Library Prep Errors

Pervasive mutations in somatic cells generate a heterogenous genomicpopulation within an organism and may result in serious medicalconditions. Next-generation sequencing (NGS) technologies have beenpivotal for the systematic identification and characterization oftumor-associated variants. While the accurate identification of lowallelic frequency somatic variants relies on factors including deepsequencing coverage, it has been found that false positive variants canaccount for more than 70% of identified somatic variations, renderingconventional detection methods inadequate for accurate determination oflow allelic variants (Chen L et al. bioRxiv 2016, 070334). Mutagenic DNAdamage has been recognized as a major source of sequencing error inspecialized samples such as FFPE-treated DNA (Do H and Dobrovic A. Clin.Chem. 2015, 61(1): 64-71). Another study indicated that a commontechnique used in sample preparation for DNA sequencing (e.g., acousticshearing in water) induces oxidative damage, including7,8-dihydro-8-oxoguanine (8-oxo-dG), suggesting that sequencing resultsmay also be affected by mutagenic damage (Costello M et al. NucleicAcids Res. 2013, 41(6): e67). Furthermore, it has been reported thatsomatic SNVs cannot be distinguished from sequencing errors, which occurat a much higher frequency than somatic mutations. Such low-abundanceSNVs and deletions have been suggested to only be able to be detectedusing single-cell sequencing, through which a heterozygous mutation willbe observed in approximately half of the reads (Zhang L and Vijg J.Annu. Rev. Genet. 2018, 52:397-419), or alternatively requiringextremely deep sequencing (e.g., 80× to up to thousands-fold coverage).

Provided herein are methods and compositions that relate to sequencingnucleic acids and determining the identity of true somatic variants fromsequencing errors. Using methods and/or compositions described herein,the complexity of the target nucleic acids is preserved by keeping trackof complementary strands after the strands have been intentionallydamaged. In order to preserve complexity of the nucleic acid,embodiments of the present disclosure relate to pairing the damagedsequences of both strands of a double-stranded nucleic acid and usingthe sequence information from both strands to distinguish low-frequencysomatic variants from sequencing errors. Briefly, nucleic acid sampleswere subjected to oxidative damage using, for example, sonication duringsample prep to intentionally introduce library prep errors. As describedsupra, oxidative damage can result in the formation of 8-oxo-dG, anoxidative damage marker introduced, for example, during acousticshearing. Alternative DNA damaging modalities may be employed, such asionizing radiation, platinum drugs (cisplatin, oxaliplatin, andcarboplatin), cyclophosphamide, chlorambucil, and temozolomide.Following intentional damage procedure, the samples contain a mixture ofknown variants and shearing-induced errors. Since 8-oxo-dG is known topair with adenine, this results in a G to T transversion afteramplification; this leads to an increase in “G to T” and “C to A”errors. As damage affects only one base of a base-pair in a duplex,acoustic shearing in water leads to an excess of G to T transversionerrors when one strand (i.e., read 1) is mapped to a reference genome,whereas, the read of the complementary strand will show an excess of thereverse complement of G to T, i.e. C to A transversion errors, instead.As a consequence, there is an imbalance in the number of G to T variantsin the first read compared to the second read sequences; see FIGS.19A-19D for an illustrative overview. This imbalance is specific to theinflicted damage and can be corrected using the methods describedherein.

Two different libraries were prepared: a first library of templatenucleic acids containing Y adapters on each end (referred to as theforked library); and a second library of Y-template-hairpin constructsprepared according to the methods described herein, for example inExample 2. Each library was subjected to three different fragmentationmethods: enzymatic (enz_frag), acoustic shearing in a TE buffer(shearTE), and acoustic shearing in water (shearWAT). Fragmentationmethod shearWAT is known to impart oxidative damage. The libraries wereamplified (see, FIGS. 19A-19D), and sequenced according to the protocolsdescribed herein, see the example workflow provided in Example 2.Sequencing can be carried out using any suitable method (e.g.,sequencing-by-synthesis) that provides suitable quality. By comparingthe reads of the two strands of the sequenced duplex it is possible tocalculate the rate of G to T errors.

The sequencing results of each individual read confirmed that acousticshearing of both the forked libraries and the Y-template-hairpinlibraries result in a greater proportion of G to T errors, relative toeach enzymatic fragmentation control. The Y-template-hairpin librariessubjected to acoustic shearing in a TE buffer did not report an increasein G to T errors. Correcting the sequencing read includesbioinformatically combining the information gained from the first readand the second read of the duplex and allows concordant base calls tobenefit from higher accuracy and removes discordant base calls.Correcting optionally further includes aligning the reads to a referencesequence. The results are summarized in terms of accuracy and Q-scorepresented in Table 3 for the Y-template-hairpin libraries sequencedherein. The quality score (Q-score) is a prediction of the probabilityof an error in base calling increases following correction. A highquality score implies that a base call is more reliable and less likelyto be incorrect.

TABLE 3 Accuracy improvement following sequencing read correction SampleName % Accuracy Q-Score enz_frag 99.4012 22.2 enz_frag (corrected)99.9743 35.9 shearTE 99.4886 22.9 shearTE (corrected) 99.9939 42.1shearWAT 99.1694 20.8 shearWAT (corrected) 99.9862 38.6

Errors introduced during library prep or during sequencing wereidentified and can be removed from the sequencing reads (i.e.,corrected), leaving only rare variants in the sequencing reads. Asreported in Table 3, the accuracy increases approximately 0.8% for theshearWAT condition as the G to T errors are identified and removed.Specifically, the G-T error rate was reduced 50-fold for these librariesafter read correction. Sequencing according to methods and constructsdescribed herein improve the accuracy, reduce false positives, and allowone to identify rare variants without increasing the sequencing readdepth. Using methods described herein, true somatic variants are thusdistinguishable from sequencing errors.

P-EMBODIMENTS

The present disclosure provides the following illustrative embodiments.

Embodiment P1. A method of sequencing a double stranded nucleic acid,the method comprising: (a) ligating a first adapter to a first end ofthe double stranded nucleic acid, and ligating a second adapter to asecond end of the double stranded nucleic acid, wherein the secondadapter is a hairpin adapter, thereby forming a nucleic acid template;(b) annealing a first primer to the nucleic acid template, wherein thefirst primer comprises a sequence that is complementary to a portion ofthe first adapter, or a complement thereof; (c) sequencing a firstportion of the nucleic acid template by extending the first primer,thereby generating a first read comprising a first nucleic acid sequenceof at least a first portion of the double stranded nucleic acid; (d)annealing a second primer to the nucleic acid template, wherein thesecond primer comprising a sequence that is complementary to a sequencewithin a loop of the hairpin adapter, or a complement thereof; and (e)sequencing a second portion of the nucleic acid template by extendingthe second primer, thereby generating a second read comprising a nucleicacid sequence of at least a second portion of the double strandednucleic acid.

Embodiment P2. The method of Embodiment P1, wherein the double strandednucleic acid comprises a forward strand and a reverse strand.

Embodiment P3. The method of Embodiment P1 or Embodiment P2, wherein thefirst adapter is a Y-adapter.

Embodiment P4. The method of Embodiment P3, wherein the Y-adaptercomprises (i) a first strand having a 5′-arm and a 3′-portion, and (ii)a second strand having a 5′-portion and a 3′-arm, wherein the 3′-portionof the first strand is substantially complementary to the 5′-portion ofthe second strand, and the 5′-arm of the first strand is notsubstantially complementary to the 3′-arm of the second strand.

Embodiment P5. The method of Embodiment P4, wherein the ligating of thefirst adapter comprises ligating a 3′-end of the first strand of theY-adapter to a 5′-end of the forward strand of the double strandednucleic acid, and ligating a 5′-end of the second strand of theY-adapter to a 3′-end of the reverse strand of the double strandednucleic acid.

Embodiment P6. The method of Embodiment P4 or Embodiment P5, wherein thefirst primer anneals to the second strand of the Y-adapter.

Embodiment P7. The method of one of Embodiment P4 to Embodiment P6,wherein the 5′-arm of the first strand or the 3′-arm of the secondstrand of the Y-adapter comprises a GC content of greater than 50%method of claim 4 or 5, wherein the first primer anneals to the secondstrand of the Y-adapter.

Embodiment P8. The method of one of Embodiment P4 to Embodiment P7,wherein the 5′-arm of the first strand or the 3′-arm of the secondstrand of the Y-adapter comprises a melting temperature (Tm) in a rangeof 60-85° C.

Embodiment P9. The method of one of Embodiment P4 to Embodiment P8,wherein the 5′-arm of the first strand or the 3′-arm of the secondstrand of the Y-adapter comprises locked nucleotides.

Embodiment P10. The method of one of Embodiment P4 to Embodiment P9,wherein the 3′-portion of the first strand or the 5′-portion of secondstrand of the Y-adapter comprises a Tm in a range of 40-50° C.

Embodiment P11. The method of one of Embodiment P4 to Embodiment P10,wherein a duplex comprising the 3′-portion of the first strand and the5′-portion of second strand of the Y-adapter comprises a Tm in a rangeof 40-50° C.

Embodiment P12. The method of one of Embodiment P4 to Embodiment P11,wherein the 3′-end or 3′-arm of the second strand of the Y-adaptercomprises a binding motif or a nucleic acid sequence complementary to afirst capture nucleic acid.

Embodiment P13. The method of one of Embodiment P4 to Embodiment P12,wherein the 5′-end or 5′-arm of the first strand of the Y-adaptercomprises a binding motif or a nucleic acid sequence substantiallyidentical to a second capture nucleic acid.

Embodiment P14. The method of one of Embodiment P4 to Embodiment P13,wherein the nucleic acid template includes sequences of the first strandof the Y-adapter, the forward strand of the double stranded nucleicacid, the second adapter, the reverse strand of the double strandednucleic acid and the second strand of the Y-adapter arranged in a 5′ to3′ direction.

Embodiment P15. The method of one of Embodiment P4 to Embodiment P14,wherein the first primer anneals to the 5′-portion of the second strandof the Y-adapter.

Embodiment P16. The method of Embodiment P1 or Embodiment P2, whereinthe first adapter is a hairpin adapter.

Embodiment P17. The method of Embodiment P16, wherein the first primeranneals to a sequence within a loop of the first adapter.

Embodiment P18. The method of one of Embodiment P2 to Embodiment P17,wherein the first read includes a nucleic acid sequence of the reversestrand of the double stranded nucleic acid, or a portion thereof, andthe second read comprises a nucleic acid sequence of the forward strandof the double stranded nucleic acid, or a portion thereof.

Embodiment P19. The method of one of Embodiment P2 to Embodiment P17,wherein the first read comprises a nucleic acid sequence of the forwardstrand of the double stranded nucleic acid, or a portion thereof, andthe second read comprises a nucleic acid sequence of the reverse strandof the double stranded nucleic acid, or a portion thereof.

Embodiment P20. The method of one of Embodiment P1 to Embodiment P19,wherein the second adapter comprises a nucleic acid having a 5′-end, a5′-portion, the loop, a 3′-portion and a 3′-end, and the 5′-portion ofthe second adapter is substantially complementary to the 3′-portion ofthe second adapter.

Embodiment P21. The method of Embodiment P20, wherein the ligating ofthe second adapter comprises ligating the 5′-end of the second adapterto a 3′-end of the forward strand of the double stranded nucleic acidand ligating the 3′-end of the second adapter to a 5′-end of the reversestrand of the double stranded nucleic acid.

Embodiment P22. The method of one of Embodiment P20 to Embodiment P21,wherein a duplex comprising the 5′-portion and the 3′-portion of thesecond adapter comprise a Tm in a range of 40-50° C.

Embodiment P23. The method of one of Embodiment P1 to Embodiment P22,wherein the first end of the double stranded nucleic acid comprises ablunt end, a 5′ overhang, or a 3′ overhang.

Embodiment P24. The method of one of Embodiment P1 to Embodiment P23,wherein the second end of the double stranded nucleic acid comprises ablunt end, a 5′ overhang, or a 3′ overhang.

Embodiment P25. The method of one of Embodiment P1 to Embodiment P24,wherein the method further comprises, after (a) and prior to (b),generating amplicons of the nucleic acid template.

Embodiment P26. The method of Embodiment P25, wherein the method ofgenerating amplicons of the nucleic acid template comprises a polymerasechain reaction.

Embodiment P27. The method of Embodiment P26, wherein the polymerasechain reaction comprises a bridge amplification method.

Embodiment P28. The method of one of Embodiment P25 to Embodiment P27,wherein the generating of amplicons comprises attaching the nucleic acidtemplate to a substrate.

Embodiment P29. The method of Embodiment P28, wherein the substrate is achip, a wafer, a bead, or a flow cell.

Embodiment P30. The method of Embodiment P28 or Embodiment P29, whereinthe substrate comprises a first capture nucleic acid comprising anucleic acid sequence complementary to at least a portion of the secondstrand of the Y-adapter, or a complement thereof.

Embodiment P31. The method of one of Embodiment P28 to Embodiment P30,wherein the attaching of the nucleic acid template to the substratecomprises annealing the nucleic acid template to the first capturenucleic acid.

Embodiment P32. The method of one of Embodiment P28 to Embodiment P31,wherein the substrate comprises a second capture nucleic acid comprisinga nucleic acid sequence complementary to at least a portion of the firststrand of the Y-adapter, or complement thereof.

Embodiment P33. The method of one of Embodiment P25 to Embodiment P32,wherein the amplicons comprise a first copy of the nucleic acid templatehaving a nucleic acid sequence that is substantially identical to thenucleic acid sequence of the nucleic acid template, or a portionthereof, and a second copy of the template having a nucleic acidsequence that is substantially complementary to the nucleic acidsequence of the nucleic acid template.

Embodiment P34. The method of Embodiment P33, wherein after generatingthe amplicons of the nucleic acid template, and before (b), the first orthe second copy of the nucleic acid template is removed from thesubstrate.

Embodiment P35. The method of one of Embodiment P25 to Embodiment P34,wherein the amplicons that are attached to the substrate are attached ataddressable locations on the substrate.

Embodiment P36. The method of Embodiment P25, wherein the generating ofamplicons comprises rolling circle amplification, and wherein the firstadapter is a hairpin adapter.

Embodiment P37. The method of one of Embodiment P1 to Embodiment P36,wherein the sequencing of (c) and the sequencing of (e) comprise aprocess comprising sequencing by synthesis.

Embodiment P38. The method of one of Embodiment P1 to Embodiment P37,wherein after step (c), the first sequenced strand is removed orterminated.

Embodiment P39. The method of one of Embodiment P1 to Embodiment P38,wherein the first adapter comprises one or more of a sample barcodesequence or a molecular identifier sequence.

Embodiment P40. The method of one of Embodiment P1 to Embodiment P39,wherein the second adapter comprises one or more of a sample barcodesequence or a molecular identifier sequence.

Embodiment P41. A method of sequencing a double stranded nucleic acid,the method comprising: (a) ligating a first adapter to a first end ofthe double stranded nucleic acid, and ligating a second adapter to asecond end of the double stranded nucleic acid, wherein the secondadapter is a hairpin adapter, thereby forming a nucleic acid template;(b) annealing a first primer to the nucleic acid template, wherein thefirst primer comprises a sequence that is complementary to a portion ofthe first adapter, or a complement thereof (c) sequencing a firstportion and a second portion of the nucleic acid template by extendingthe first primer, thereby generating a first read comprising a firstnucleic acid sequence of at least a first portion of the double strandednucleic acid, and a second read comprising a nucleic acid sequence of atleast a second portion of the double stranded nucleic acid.

Embodiment P42. A multiplex method of sequencing a plurality of doublestranded nucleic acids comprising one of the methods of Embodiment P1 toEmbodiment P41, comprising performing steps (a) through (e) for each ofa plurality of double-stranded nucleic acids in a mixture.

Embodiment P43. A composition for sequencing a double stranded nucleicacid comprising a forward strand and a reverse strand, the compositioncomprising a template nucleic acid comprising sequences of a firststrand of a Y-adapter, the forward strand of the double stranded nucleicacid, a hairpin adapter, the reverse strand of the double strandednucleic acid and a second strand of the Y-adapter arranged in a 5′ to 3′direction, wherein the template is attached to a substrate.

Embodiment P44. The composition of Embodiment P43, further comprising(ii) a primer hybridized to a loop of the hairpin adapter.

Embodiment P45. A kit for sequencing a double stranded nucleic acid,comprising: (i) a first adapter, wherein the first adapter comprises adouble-stranded portion and at least one single-stranded portion; (ii) asecond adapter, wherein the second adapter is a hairpin adaptercomprising a nucleic acid having a 5′-end, a 5′-portion, a loop, a3′-portion and a 3′-end, and the 5′-portion of the hairpin adapter issubstantially complementary to the 3′-portion of the hairpin adapter;(iii) a first primer having a nucleic acid sequence complementary to aportion of the first adapter, or a complement thereof; and (iv) a secondprimer having a nucleic acid sequence complementary to the loop of thehairpin adapter, or a complement thereof.

Embodiment P46. The kit of Embodiment P45, wherein the first adapter isa Y-adapter, wherein the Y-adapter comprises (i) a first strand having a5′-portion and a 3′-portion, and (ii) a second strand having a5′-portion and a 3′-portion, wherein the 3′-portion of the first strandis substantially complementary to the 5′-portion of the second strand,and the 5′-portion of the first strand is not substantiallycomplementary to the 3′-portion of the second strand.

Embodiment P47. The kit of Embodiment P46, wherein the first adapter isa hairpin adapter.

Embodiment P48. A method of selectively sequencing a double-strandednucleic acid, the method comprising: (a) ligating a first adapter to afirst end of the double-stranded nucleic acid, and ligating a secondadapter to a second end of the double-stranded nucleic acid, wherein thesecond adapter is a hairpin adapter; (b) displacing at least a portionof one strand of the double-stranded nucleic acid from step (a); (c)hybridizing a probe oligonucleotide to the displaced portion of thedouble-stranded nucleic acid; (d) separating the probe-hybridizeddouble-stranded nucleic acid from nucleic acids not hybridized to aprobe; and (e) sequencing the probe-hybridized double-stranded nucleicacid of step (d).

Embodiment P49. The method of Embodiment P48, wherein the first adapteris a Y-adapter, and the displacing at least a portion of one strand ofthe double-stranded nucleic acid comprises: (i) hybridizing a primer toa single-stranded portion of the Y-adapter, and (ii) in a primerextension reaction, extending the primer with a strand-displacingpolymerase that terminates extension within a loop of the hairpinadapter at a terminating nucleotide.

Embodiment P50. The method of Embodiment P48, wherein the first adapteris a hairpin adapter, and the displacing at least a portion of onestrand of the double-stranded nucleic acid comprises: (i) hybridizing aprimer within a loop of the first hairpin adapter, and (ii) in a primerextension reaction, extending the primer with a strand-displacingpolymerase that terminates extension within a loop of the second hairpinadapter at a terminating nucleotide.

Embodiment P51. The method of Embodiment P49 or Embodiment P50, whereinthe terminating nucleotide comprises a removable group that blocksprogression of the strand-displacing polymerase, and further wherein theterminating nucleotide is treated to release the removable group priorto sequencing.

Embodiment P52. The method of Embodiment P51, wherein the removablegroup is a polymer or a protein joined to the terminating nucleotide bya cleavable linker.

Embodiment P53. The method of Embodiment P51, wherein the removablegroup is a protein that is non-covalently complexed to the terminatingnucleotide, and further wherein releasing the protein comprises a changein reaction conditions to disrupt the complex.

Embodiment P54. The method of Embodiment P53, wherein (i) the protein isa first member of a binding pair complexed with a second member of thebinding pair that is linked to the terminating nucleotide, or (ii) theprotein is a single-stranded binding protein that recognizes a sequencewithin the loop of the hairpin adapter.

Embodiment P55. The method of Embodiment P49 or Embodiment P50, wherein(i) the terminating nucleotide is a first nucleotide analog that basepairs with a second nucleotide analog, and (ii) the second nucleotideanalog is not present in the primer extension reaction, such that primerextension terminates.

Embodiment P56. The method of Embodiment P49 or Embodiment P50, whereinthe terminating nucleotide is an RNA nucleotide.

Embodiment P57. The method of Embodiment P48, wherein the first adapteris a Y-adapter, and the displacing at least a portion of one strand ofthe double-stranded nucleic acid comprises: (i) hybridizing a primerwithin a loop of the hairpin adapter, and (ii) in a primer extensionreaction, extending the primer with a strand-displacing polymerase.

Embodiment P58. The method of Embodiment P48, wherein the first adapteris a hairpin adapter, and the displacing at least a portion of onestrand of the double-stranded nucleic acid comprises: (i) hybridizing aprimer within a loop of the hairpin adapter, and (ii) in a primerextension reaction, extending the primer with a strand-displacingpolymerase.

Embodiment P59. The method of Embodiment P48, wherein the displacing atleast a portion of one strand of the double-stranded nucleic acidcomprises (i) forming a complex comprising a portion of thedouble-stranded nucleic acid, a primer, and a homologous recombinationcomplex comprising a recombinase, (ii) releasing the recombinase, and(iii) in a primer extension reaction, extending the primer with astrand-displacing polymerase.

Embodiment P60. The method of Embodiment P48, wherein (i) the displacingat least a portion of one strand of the double-stranded nucleic acidcomprises forming a complex comprising a portion of the double-strandednucleic acid, the probe oligonucleotide, and a homologous recombinationcomplex comprising a recombinase, and (ii) the step of hybridizing theprobe oligonucleotide comprises releasing the recombinase.

Embodiment P61. The method of Embodiment P59 or Embodiment P60, whereinthe homologous recombination complex further comprises a loading factor,a single-stranded binding (SSB) protein, or both.

Embodiment P62. The method of one of Embodiment P59 to Embodiment P61,wherein the recombinase is a T4 UvsX, RecA, or Rad51 protein.

Embodiment P63. The method of Embodiment P61 or Embodiment P62, whereinthe loading factor comprises a T4 UvsY protein.

Embodiment P64. The method of Embodiment P48, wherein the displacing atleast a portion of one strand of the double-stranded nucleic acidcomprises exposing the double-stranded nucleic acid to denaturingconditions.

Embodiment P65. The method of one of Embodiment P48 to Embodiment P64,wherein the probe oligonucleotide is covalently attached to a solidsubstrate.

Embodiment P66. The method of one of Embodiment P48 to Embodiment P64,wherein the probe oligonucleotide is labeled with a first member of abinding pair, and the step of separating the probe-hybridizeddouble-stranded nucleic acid comprises capturing the probe with a secondmember of the binding pair.

Embodiment P67. The method of Embodiment P66, wherein (i) the firstmember of the binding pair is biotin and the second member of thebinding pair is avidin or streptavidin, or (ii) the second member of thebinding pair is biotin and the first member of the binding pair isavidin or streptavidin.

Embodiment P68. The method of one of Embodiment P48 to Embodiment P67,wherein the probe is complementary to 10, 15, 20, 25, 50, 75, 120, ormore consecutive nucleotides of the displaced portion of thedouble-stranded nucleic acid.

Embodiment P69. The method of Embodiment P64, wherein the probe iscomplementary to 100, 120, or more consecutive nucleotides of thedisplaced portion of the double-stranded nucleic acid.

Embodiment P70. The method of one of Embodiment P48 to Embodiment P69,wherein the double-stranded nucleic acid is a cell-free DNA (cfDNA) orcirculating tumor DNA (ctDNA).

Embodiment P71. A method of selectively sequencing a plurality ofdifferent double-stranded nucleic acids in a sample according to amethod of one of Embodiment P48 to Embodiment P70, wherein a pluralityof different probe oligonucleotides are utilized during the hybridizingstep.

Embodiment P72. The method of one of Embodiment P48 to Embodiment P71,wherein the sequencing comprises sequencing according to the method ofone of Embodiment P1 to Embodiment P42.

Additional Embodiments

The present disclosure provides the following additional illustrativeembodiments.

Embodiment 1. A method of sequencing a double stranded nucleic acid, themethod comprising: (a) ligating a first adapter to a first end of thedouble stranded nucleic acid, and ligating a second adapter to a secondend of the double stranded nucleic acid, wherein the second adapter is ahairpin adapter, thereby forming a nucleic acid template; (b) annealinga first primer to the nucleic acid template, wherein the first primercomprises a sequence that is complementary to a portion of the firstadapter, or a complement thereof; (c) sequencing a first portion of thenucleic acid template by extending the first primer, thereby generatinga first read comprising a first nucleic acid sequence of at least afirst portion of the double stranded nucleic acid; (d) annealing asecond primer to the nucleic acid template, wherein the second primercomprising a sequence that is complementary to a sequence within a loopof the hairpin adapter, or a complement thereof; and (e) sequencing asecond portion of the nucleic acid template by extending the secondprimer, thereby generating a second read comprising a nucleic acidsequence of at least a second portion of the double stranded nucleicacid.Embodiment 2. The method of embodiment 1, wherein the double strandednucleic acid comprises a forward strand and a reverse strand.Embodiment 3. The method of embodiment 1 or 2, wherein the first adapteris a Y-adapter.Embodiment 4. The method of embodiment 3, wherein the Y-adaptercomprises (i) a first strand having a 5′-arm and a 3′-portion, and (ii)a second strand having a 5′-portion and a 3′-arm, wherein the 3′-portionof the first strand is substantially complementary to the 5′-portion ofthe second strand, and the 5′-arm of the first strand is notsubstantially complementary to the 3′-arm of the second strand.Embodiment 5. The method of embodiment 4, wherein the ligating of thefirst adapter comprises ligating a 3′-end of the first strand of theY-adapter to a 5′-end of the forward strand of the double strandednucleic acid, and ligating a 5′-end of the second strand of theY-adapter to a 3′-end of the reverse strand of the double strandednucleic acid.Embodiment 6. The method of embodiment 4 or 5, wherein the first primeranneals to the second strand of the Y-adapter.Embodiment 7. The method of any one of embodiments 4 to 6, wherein the5′-arm of the first strand or the 3′-arm of the second strand of theY-adapter comprises a GC content of greater than 50%.method of claim 4or 5, wherein the first primer anneals to the second strand of theY-adapter.Embodiment 8. The method of any one of embodiments 4 to 7, wherein the5′-arm of the first strand or the 3′-arm of the second strand of theY-adapter comprises a melting temperature (Tm) in a range of 60-85° C.Embodiment 9. The method of any one of embodiments 4 to 8, wherein the5′-arm of the first strand or the 3′-arm of the second strand of theY-adapter comprises locked nucleotides.Embodiment 10. The method of any one of embodiments 4 to 9, wherein the3′-portion of the first strand or the 5′-portion of second strand of theY-adapter comprises a Tm in a range of 40-50° C.Embodiment 11. The method of any one of embodiments 4 to 10, wherein aduplex comprising the 3′-portion of the first strand and the 5′-portionof second strand of the Y-adapter comprises a Tm in a range of 40-50° C.Embodiment 12. The method of any one of embodiments 4 to 11, wherein the3′-end or 3′-arm of the second strand of the Y-adapter comprises abinding motif or a nucleic acid sequence complementary to a firstcapture nucleic acid.Embodiment 13. The method of any one of embodiments 4 to 12, wherein the5′-end or 5′-arm of the first strand of the Y-adapter comprises abinding motif or a nucleic acid sequence substantially identical to asecond capture nucleic acid.Embodiment 14. The method of any one of embodiments 4 to 13, wherein thenucleic acid template includes sequences of the first strand of theY-adapter, the forward strand of the double stranded nucleic acid, thesecond adapter, the reverse strand of the double stranded nucleic acidand the second strand of the Y-adapter arranged in a 5′ to 3′ direction.Embodiment 15. The method of any one of embodiments 4 to 14, wherein thefirst primer anneals to the 5′-portion of the second strand of theY-adapter.Embodiment 16. The method of embodiment 1 or 2, wherein the firstadapter is a hairpin adapter.Embodiment 17. The method of embodiment 16, wherein the first primeranneals to a sequence within a loop of the first adapter.Embodiment 18. The method of any one of embodiments 2 to 17, wherein thefirst read includes a nucleic acid sequence of the reverse strand of thedouble stranded nucleic acid, or a portion thereof, and the second readcomprises a nucleic acid sequence of the forward strand of the doublestranded nucleic acid, or a portion thereof.Embodiment 19. The method of any one of embodiments 2 to 17, wherein thefirst read comprises a nucleic acid sequence of the forward strand ofthe double stranded nucleic acid, or a portion thereof, and the secondread comprises a nucleic acid sequence of the reverse strand of thedouble stranded nucleic acid, or a portion thereof.Embodiment 20. The method of any one of embodiments 1 to 19, wherein thesecond adapter comprises a nucleic acid having a 5′-end, a 5′-portion,the loop, a 3′-portion and a 3′-end, and the 5′-portion of the secondadapter is substantially complementary to the 3′-portion of the secondadapter.Embodiment 21. The method of embodiment 20, wherein the ligating of thesecond adapter comprises ligating the 5′-end of the second adapter to a3′-end of the forward strand of the double stranded nucleic acid andligating the 3′-end of the second adapter to a 5′-end of the reversestrand of the double stranded nucleic acid.Embodiment 22. The method of any one of embodiments 20 to 21, wherein aduplex comprising the 5′-portion and the 3′-portion of the secondadapter comprise a Tm in a range of 40-50° C.Embodiment 23. The method of any one of embodiments 1 to 22, wherein thefirst end of the double stranded nucleic acid comprises a blunt end, a5′ overhang, or a 3′ overhang.Embodiment 24. The method of any one of embodiments 1 to 23, wherein thesecond end of the double stranded nucleic acid comprises a blunt end, a5′ overhang, or a 3′ overhang.Embodiment 25. The method of any one of embodiments 1 to 24, wherein themethod further comprises, after (a) and prior to (b), generatingamplicons of the nucleic acid template.Embodiment 26. The method of embodiment 25, wherein the method ofgenerating amplicons of the nucleic acid template comprises a polymerasechain reaction.Embodiment 27. The method of embodiment 26, wherein the polymerase chainreaction comprises a bridge amplification method.Embodiment 28. The method of any one of embodiments 25 to 27, whereinthe generating of amplicons comprises attaching the nucleic acidtemplate to a substrate.Embodiment 29. The method of embodiment 28, wherein the substrate is achip, a wafer, a bead, or a flow cell.Embodiment 30. The method of embodiment 28 or 29, wherein the substratecomprises a first capture nucleic acid comprising a nucleic acidsequence complementary to at least a portion of the second strand of theY-adapter, or a complement thereof.Embodiment 31. The method of any one of embodiments 28 to 30, whereinthe attaching of the nucleic acid template to the substrate comprisesannealing the nucleic acid template to the first capture nucleic acid.Embodiment 32. The method of any one of embodiments 28 to 31, whereinthe substrate comprises a second capture nucleic acid comprising anucleic acid sequence complementary to at least a portion of the firststrand of the Y-adapter, or complement thereof.Embodiment 33. The method of any one of embodiments 25 to 32, whereinthe amplicons comprise a first copy of the nucleic acid template havinga nucleic acid sequence that is substantially identical to the nucleicacid sequence of the nucleic acid template, or a portion thereof, and asecond copy of the template having a nucleic acid sequence that issubstantially complementary to the nucleic acid sequence of the nucleicacid template.Embodiment 34. The method of embodiment 33, wherein after generating theamplicons of the nucleic acid template, and before (b), the first or thesecond copy of the nucleic acid template is removed from the substrate.Embodiment 35. The method of any one of embodiments 25 to 34, whereinthe amplicons that are attached to the substrate are attached ataddressable locations on the substrate.Embodiment 36. The method of embodiment 25, wherein the generating ofamplicons comprises rolling circle amplification, and wherein the firstadapter is a hairpin adapter.Embodiment 37. The method of any one of embodiments 1 to 36, wherein thesequencing of (c) and the sequencing of (e) comprise a processcomprising sequencing by synthesis.Embodiment 38. The method of any one of embodiments 1 to 37, whereinafter step (c), the first sequenced strand is removed or terminated.Embodiment 39. The method of any one of embodiments 1 to 38, wherein thefirst adapter comprises one or more of a sample barcode sequence or amolecular identifier sequence.Embodiment 40. The method of any one of embodiments 1 to 39, wherein thesecond adapter comprises one or more of a sample barcode sequence or amolecular identifier sequence.Embodiment 41. A method of sequencing a double stranded nucleic acid,the method comprising: (a) ligating a first adapter to a first end ofthe double stranded nucleic acid, and ligating a second adapter to asecond end of the double stranded nucleic acid, wherein the secondadapter is a hairpin adapter, thereby forming a nucleic acid template;(b) annealing a first primer to the nucleic acid template, wherein thefirst primer comprises a sequence that is complementary to a portion ofthe first adapter, or a complement thereof; (c) sequencing a firstportion and a second portion of the nucleic acid template by extendingthe first primer, thereby generating a first read comprising a firstnucleic acid sequence of at least a first portion of the double strandednucleic acid, and a second read comprising a nucleic acid sequence of atleast a second portion of the double stranded nucleic acid.Embodiment 42. A multiplex method of sequencing a plurality of doublestranded nucleic acids comprising any one of the methods of embodiments1 to 41, comprising performing steps (a) through (e) for each of aplurality of double-stranded nucleic acids in a mixture.Embodiment 43. A composition for sequencing a double stranded nucleicacid comprising a forward strand and a reverse strand, the compositioncomprising a template nucleic acid comprising sequences of a firststrand of a Y-adapter, the forward strand of the double stranded nucleicacid, a hairpin adapter, the reverse strand of the double strandednucleic acid and a second strand of the Y-adapter arranged in a 5′ to 3′direction, wherein the template is attached to a substrate.Embodiment 44. The composition of embodiment 43, further comprising (ii)a primer hybridized to a loop of the hairpin adapter.Embodiment 45. A kit for sequencing a double stranded nucleic acid,comprising: (i) a first adapter, wherein the first adapter comprises adouble-stranded portion and at least one single-stranded portion; (ii) asecond adapter, wherein the second adapter is a hairpin adaptercomprising a nucleic acid having a 5′-end, a 5′-portion, a loop, a3′-portion and a 3′-end, and the 5′-portion of the hairpin adapter issubstantially complementary to the 3′-portion of the hairpin adapter;(iii) a first primer having a nucleic acid sequence complementary to aportion of the first adapter, or a complement thereof; and (iv) a secondprimer having a nucleic acid sequence complementary to the loop of thehairpin adapter, or a complement thereof.Embodiment 46. The kit of embodiment 45, wherein the first adapter is aY-adapter, wherein the Y-adapter comprises (i) a first strand having a5′-portion and a 3′-portion, and (ii) a second strand having a5′-portion and a 3′-portion, wherein the 3′-portion of the first strandis substantially complementary to the 5′-portion of the second strand,and the 5′-portion of the first strand is not substantiallycomplementary to the 3′-portion of the second strand.Embodiment 47. The kit of embodiment 46, wherein the first adapter is ahairpin adapter.Embodiment 48. A method of selectively sequencing a double-strandednucleic acid, the method comprising: (a) ligating a first adapter to afirst end of the double-stranded nucleic acid, and ligating a secondadapter to a second end of the double-stranded nucleic acid, wherein thesecond adapter is a hairpin adapter; (b) displacing at least a portionof one strand of the double-stranded nucleic acid from step (a); (c)hybridizing a probe oligonucleotide to the displaced portion of thedouble-stranded nucleic acid; (d) separating the probe-hybridizeddouble-stranded nucleic acid from nucleic acids not hybridized to aprobe; and (e) sequencing the probe-hybridized double-stranded nucleicacid of step (d).Embodiment 49. The method of embodiment 48, wherein the first adapter isa Y-adapter, and the displacing at least a portion of one strand of thedouble-stranded nucleic acid comprises: (i) hybridizing a primer to asingle-stranded portion of the Y-adapter, and (ii) in a primer extensionreaction, extending the primer with a strand-displacing polymerase thatterminates extension within a loop of the hairpin adapter at aterminating nucleotide.Embodiment 50. The method of embodiment 48, wherein the first adapter isa hairpin adapter, and the displacing at least a portion of one strandof the double-stranded nucleic acid comprises: (i) hybridizing a primerwithin a loop of the first hairpin adapter, and (ii) in a primerextension reaction, extending the primer with a strand-displacingpolymerase that terminates extension within a loop of the second hairpinadapter at a terminating nucleotide.Embodiment 51. The method of embodiment 49 or 50, wherein theterminating nucleotide comprises a removable group that blocksprogression of the strand-displacing polymerase, and further wherein theterminating nucleotide is treated to release the removable group priorto sequencing.Embodiment 52. The method of embodiment 51, wherein the removable groupis a polymer or a protein joined to the terminating nucleotide by acleavable linker.Embodiment 53. The method of embodiment 51, wherein the removable groupis a protein that is non-covalently complexed to the terminatingnucleotide, and further wherein releasing the protein comprises a changein reaction conditions to disrupt the complex.Embodiment 54. The method of embodiment 53, wherein (i) the protein is afirst member of a binding pair complexed with a second member of thebinding pair that is linked to the terminating nucleotide, or (ii) theprotein is a single-stranded binding protein that recognizes a sequencewithin the loop of the hairpin adapter.Embodiment 55. The method of embodiment 49 or 50, wherein (i) theterminating nucleotide is a first nucleotide analog that base pairs witha second nucleotide analog, and (ii) the second nucleotide analog is notpresent in the primer extension reaction, such that primer extensionterminates.Embodiment 56. The method of embodiment 49 or 50, wherein theterminating nucleotide is an RNA nucleotide.Embodiment 57. The method of embodiment 48, wherein the first adapter isa Y-adapter, and the displacing at least a portion of one strand of thedouble-stranded nucleic acid comprises: (i) hybridizing a primer withina loop of the hairpin adapter, and (ii) in a primer extension reaction,extending the primer with a strand-displacing polymerase.Embodiment 58. The method of embodiment 48, wherein the first adapter isa hairpin adapter, and the displacing at least a portion of one strandof the double-stranded nucleic acid comprises: (i) hybridizing a primerwithin a loop of the hairpin adapter, and (ii) in a primer extensionreaction, extending the primer with a strand-displacing polymerase.Embodiment 59. The method of embodiment 48, wherein the displacing atleast a portion of one strand of the double-stranded nucleic acidcomprises (i) forming a complex comprising a portion of thedouble-stranded nucleic acid, a primer, and a homologous recombinationcomplex comprising a recombinase, (ii) releasing the recombinase, and(iii) in a primer extension reaction, extending the primer with astrand-displacing polymerase.Embodiment 60. The method of embodiment 48, wherein (i) the displacingat least a portion of one strand of the double-stranded nucleic acidcomprises forming a complex comprising a portion of the double-strandednucleic acid, the probe oligonucleotide, and a homologous recombinationcomplex comprising a recombinase, and (ii) the step of hybridizing theprobe oligonucleotide comprises releasing the recombinase.Embodiment 61. The method of embodiment 59 or 60, wherein the homologousrecombination complex further comprises a loading factor, asingle-stranded binding (SSB) protein, or both.Embodiment 62. The method of any one of embodiments 59 to 61, whereinthe recombinase is a T4 UvsX, RecA, or Rad51 protein.Embodiment 63. The method of embodiment 61 or 62, wherein the loadingfactor comprises a T4 UvsY protein.Embodiment 64. The method of embodiment 48, wherein the displacing atleast a portion of one strand of the double-stranded nucleic acidcomprises exposing the double-stranded nucleic acid to denaturingconditions.Embodiment 65. The method of any one of embodiments 48 to 64, whereinthe probe oligonucleotide is covalently attached to a solid substrate.Embodiment 66. The method of any one of embodiments 48 to 64, whereinthe probe oligonucleotide is labeled with a first member of a bindingpair, and the step of separating the probe-hybridized double-strandednucleic acid comprises capturing the probe with a second member of thebinding pair.Embodiment 67. The method of embodiment 66, wherein (i) the first memberof the binding pair is biotin and the second member of the binding pairis avidin or streptavidin, or (ii) the second member of the binding pairis biotin and the first member of the binding pair is avidin orstreptavidin.Embodiment 68. The method of any one of embodiments 48 to 67, whereinthe probe is complementary to 10, 15, 20, 25, 50, 75, 120, or moreconsecutive nucleotides of the displaced portion of the double-strandednucleic acid.Embodiment 69. The method of embodiment 64, wherein the probe iscomplementary to 100, 120, or more consecutive nucleotides of thedisplaced portion of the double-stranded nucleic acid.Embodiment 70. The method of any one of embodiments 48 to 69, whereinthe double-stranded nucleic acid is a cell-free DNA (cfDNA) orcirculating tumor DNA (ctDNA).Embodiment 71. A method of selectively sequencing a plurality ofdifferent double-stranded nucleic acids in a sample according to amethod of any one of embodiments 48 to 70, wherein a plurality ofdifferent probe oligonucleotides are utilized during the hybridizingstep.Embodiment 72. The method of any one of embodiments 48 to 71, whereinthe sequencing comprises sequencing according to the method of any oneof embodiments 1 to 42.Embodiment 73. A method of sequencing a double stranded nucleic acidcomprising one or more methylated cytosines, the method comprising: (a)ligating a first adapter to a first end of the double stranded nucleicacid, and ligating a second adapter to a second end of the doublestranded nucleic acid, wherein the second adapter is a hairpin adapter,thereby forming a nucleic acid template; (b) converting one or morecytosines to uracil; (c) annealing a first primer to the nucleic acidtemplate, wherein the first primer comprises a sequence that iscomplementary to a portion of the first adapter, or a complementthereof; (d) sequencing a first portion of the nucleic acid template byextending the first primer, thereby generating a first read comprising afirst nucleic acid sequence of at least a first portion of the doublestranded nucleic acid; (e) annealing a second primer to the nucleic acidtemplate, wherein the second primer comprises a sequence that iscomplementary to a sequence within a loop of the hairpin adapter, or acomplement thereof; and (f) sequencing a second portion of the nucleicacid template by extending the second primer, thereby generating asecond read comprising a nucleic acid sequence of at least a secondportion of the double stranded nucleic acid.Embodiment 74. The method of Embodiment 74, wherein the first adaptercomprises one or more methylated cytosines.Embodiment 75. The method of Embodiment 73 or 74, wherein the secondadapter comprises one or more methylated cytosines.Embodiment 76. The method of one of Embodiments 73-75, whereinconverting the one or more cytosines to uracil comprises chemical orenzymatic conversion.Embodiment. 77. A method of amplifying a double stranded nucleic acidcomprising a first strand and a second strand, the method comprising:(a) ligating a first adapter to a first end of the double strandednucleic acid wherein the first adapter is a Y adapter comprising (i) afirst strand having a 5′-arm and a 3′-portion, and (ii) a second strandhaving a 5′-portion and a 3′-arm, wherein the 3′-portion of the firststrand is substantially complementary to the 5′-portion of the secondstrand, and the 5′-arm of the first strand is not substantiallycomplementary to the 3′-arm of the second strand, and ligating a secondadapter to a second end of the double stranded nucleic acid, wherein thesecond adapter is a hairpin adapter, thereby forming a nucleic acidtemplate; (b) annealing a primer to the nucleic acid template, whereinthe first primer comprises a sequence that is complementary to a portionof the first adapter, or a complement thereof, and is not substantiallycomplementary to a portion of the second adapter or a complementthereof; (c) amplifying the nucleic acid template by extending theprimer using a strand-displacing polymerase, thereby generating a anamplicon comprising a complement of the first and second strand of thedouble stranded nucleic acid.Embodiment 78. The method of Embodiment 77, wherein amplifying thenucleic acid template is on a solid support comprising a plurality ofprimers attached to said solid support, wherein the plurality of primerscomprise a plurality of forward primers with complementarity to acomplement of the first strand of the Y adapter and a plurality ofreverse primers with complementarity to the second strand of the Yadapter, and the amplifying comprises a plurality of cycles of stranddenaturation, primer hybridization, and primer extension, therebygenerating a plurality of forward amplicons and a plurality of reverseamplicons.Embodiment 79. The method of Embodiment 78, further comprising removingthe plurality of reverse amplicons or forward amplicons, annealing aprimer to the first amplicon, wherein the first primer comprises asequence that is complementary to a portion of the first amplicon, or acomplement thereof, and sequencing a portion of the first amplicon byextending the primer, thereby generating a sequencing read comprising afirst nucleic acid sequence of at least a first portion of the doublestranded nucleic acid.Embodiment 80. A method of sequencing a first portion and a secondportion of a double-stranded nucleic acid, the method comprising: (a)ligating a first adapter to a first end of the double stranded nucleicacid, and ligating a second adapter to a second end of the doublestranded nucleic acid, wherein the second adapter is a hairpin adapter,thereby forming a nucleic acid template; (b) displacing at least aportion of one strand of the nucleic acid template by annealing ablocking primer to the nucleic acid template and extending the blockingprimer to generate a blocking strand, wherein the blocking primercomprises a sequence within a loop of the hairpin adapter, or acomplement thereof (c) annealing a first sequencing primer to thenucleic acid template and sequencing a first portion of the nucleic acidtemplate by extending the first sequencing primer, thereby generating afirst read comprising a first nucleic acid sequence of at least a firstportion of the double stranded nucleic acid, wherein the firstsequencing primer comprises a sequence that is complementary to aportion of the first adapter; (d) annealing a second sequencing primerto the nucleic acid template and sequencing a second portion of thenucleic acid template by extending the second sequencing primer, therebygenerating a second read comprising a second nucleic acid sequence of atleast a second portion of the double stranded nucleic acid, wherein thesecond sequencing primer comprises a sequence that is complementary to asequence within a loop of the hairpin adapter, or a complement thereof.Embodiment 81. The method of Embodiment 80, wherein the second adaptercomprises a cleavable site.Embodiment 82. The method of Embodiments 80 or 81, wherein the blockingstrand is removed prior to step d).Embodiment 83. The method of any one of Embodiments 80 to 82, whereinthe extended sequencing primer from step c) is removed prior to step d).Embodiment 84. The method of any one of Embodiments 80 to 83, whereinsequencing the first portion and a second portion of a double-strandednucleic acid is on a solid support comprising a plurality of primersattached to said solid support, wherein the plurality of primerscomprise a plurality of forward primers with complementarity to acomplement of the first strand of the Y adapter and a plurality ofreverse primers with complementarity to the second strand of the Yadapter.

1. A method of sequencing a double stranded nucleic acid, the methodcomprising: (a) ligating a first adapter to a first end of the doublestranded nucleic acid, and ligating a second adapter to a second end ofthe double stranded nucleic acid, wherein the second adapter is ahairpin adapter, thereby forming a nucleic acid template; (b) annealinga first primer to the nucleic acid template, wherein the first primercomprises a sequence that is complementary to a portion of the firstadapter, or a complement thereof; (c) sequencing a first portion of thenucleic acid template by extending the first primer, thereby generatinga first read comprising a first nucleic acid sequence of at least afirst portion of the double stranded nucleic acid; (d) annealing asecond primer to the nucleic acid template, wherein the second primercomprises a sequence that is complementary to a sequence within a loopof the hairpin adapter, or a complement thereof; and (e) sequencing asecond portion of the nucleic acid template by extending the secondprimer, thereby generating a second read comprising a nucleic acidsequence of at least a second portion of the double stranded nucleicacid.
 2. (canceled)
 3. The method of claim 1, wherein the first adapteris a Y-adapter, wherein the Y-adapter comprises (i) a first strandhaving a 5′-arm and a 3′-portion, and (ii) a second strand having a5′-portion and a 3′-arm, wherein the 3′-portion of the first strand issubstantially complementary to the 5′-portion of the second strand, andthe 5′-arm of the first strand is not substantially complementary to the3′-arm of the second strand.
 4. (canceled)
 5. The method of claim 3,wherein the ligating of the first adapter comprises ligating a 3′-end ofthe first strand of the Y-adapter to a 5′-end of the forward strand ofthe double stranded nucleic acid, and ligating a 5′-end of the secondstrand of the Y-adapter to a 3′-end of the reverse strand of the doublestranded nucleic acid.
 6. The method of claim 3, wherein the firstprimer anneals to the second strand of the Y-adapter. 7-15. (canceled)16. The method of claim 1, wherein the first adapter is a hairpinadapter.
 17. The method of claim 16, wherein the first primer anneals toa sequence within a loop of the first adapter. 18-19. (canceled)
 20. Themethod of claim 1, wherein the second adapter comprises a nucleic acidhaving a 5′-end, a 5′-portion, the loop, a 3′-portion and a 3′-end, andthe 5′-portion of the second adapter is substantially complementary tothe 3′-portion of the second adapter.
 21. The method of claim 20,wherein the ligating of the second adapter comprises ligating the 5′-endof the second adapter to a 3′-end of the forward strand of the doublestranded nucleic acid and ligating the 3′-end of the second adapter to a5′-end of the reverse strand of the double stranded nucleic acid.22.-24. (canceled)
 25. The method of claim 1, wherein the method furthercomprises, after (a) and prior to (b), generating amplicons of thenucleic acid template.
 26. The method of claim 25, wherein the method ofgenerating amplicons of the nucleic acid template comprises a polymerasechain reaction.
 27. The method of claim 26, wherein the polymerase chainreaction comprises a bridge PCR amplification method. 28-35. (canceled)36. The method of claim 25, wherein the generating of ampliconscomprises rolling circle amplification, and wherein the first adapter isa hairpin adapter.
 37. The method of claim 1, wherein the sequencing of(c) and the sequencing of (e) comprise a process comprising sequencingby synthesis.
 38. (canceled)
 39. The method of claim 1, wherein thefirst adapter comprises one or more of a sample barcode sequence, amolecular identifier sequence, or both a sample barcode sequence and amolecular identifier sequence.
 40. The method of claim 1, wherein thesecond adapter comprises one or more of a sample barcode sequence, amolecular identifier sequence, or both a sample barcode sequence and amolecular identifier sequence. 41-47. (canceled)
 48. A method ofselectively sequencing a double-stranded nucleic acid, the methodcomprising: (a) ligating a first adapter to a first end of thedouble-stranded nucleic acid, and ligating a second adapter to a secondend of the double-stranded nucleic acid, wherein the second adapter is ahairpin adapter; (b) displacing at least a portion of one strand of thedouble-stranded nucleic acid from step (a); (c) hybridizing a probeoligonucleotide to the displaced portion of the double-stranded nucleicacid; (d) separating the probe-hybridized double-stranded nucleic acidfrom nucleic acids not hybridized to a probe; and (e) sequencing theprobe-hybridized double-stranded nucleic acid of step (d).
 49. Themethod of claim 48, wherein the first adapter is a Y-adapter, and thedisplacing at least a portion of one strand of the double-strandednucleic acid comprises: (i) hybridizing a primer to a single-strandedportion of the Y-adapter, and (ii) in a primer extension reaction,extending the primer with a strand-displacing polymerase that terminatesextension within a loop of the hairpin adapter at a terminatingnucleotide.
 50. The method of claim 48, wherein the first adapter is ahairpin adapter, and the displacing at least a portion of one strand ofthe double-stranded nucleic acid comprises: (i) hybridizing a primerwithin a loop of the first hairpin adapter, and (ii) in a primerextension reaction, extending the primer with a strand-displacingpolymerase that terminates extension within a loop of the second hairpinadapter at a terminating nucleotide.
 51. The method of claim 49, whereinthe terminating nucleotide comprises a removable group that blocksprogression of the strand-displacing polymerase, and further wherein theterminating nucleotide is treated to release the removable group priorto sequencing.
 52. The method of claim 51, wherein the removable groupis a polymer or a protein joined to the terminating nucleotide by acleavable linker. 53.-56. (canceled)
 57. The method of claim 48, whereinthe first adapter is a Y-adapter, and the displacing at least a portionof one strand of the double-stranded nucleic acid comprises: (i)hybridizing a primer within a loop of the hairpin adapter, and (ii) in aprimer extension reaction, extending the primer with a strand-displacingpolymerase.
 58. The method of claim 48, wherein the first adapter is ahairpin adapter, and the displacing at least a portion of one strand ofthe double-stranded nucleic acid comprises: (i) hybridizing a primerwithin a loop of the hairpin adapter, and (ii) in a primer extensionreaction, extending the primer with a strand-displacing polymerase. 59.The method of claim 48, wherein the displacing at least a portion of onestrand of the double-stranded nucleic acid comprises (i) forming acomplex comprising a portion of the double-stranded nucleic acid, aprimer, and a homologous recombination complex comprising a recombinase,(ii) releasing the recombinase, and (iii) in a primer extensionreaction, extending the primer with a strand-displacing polymerase.60.-63. (canceled)
 64. The method of claim 48, wherein the displacing atleast a portion of one strand of the double-stranded nucleic acidcomprises exposing the double-stranded nucleic acid to denaturingconditions.
 65. The method of claim 48, wherein the probeoligonucleotide is covalently attached to a solid substrate. 66.-67.(canceled)
 68. The method of claim 48, wherein the probe iscomplementary to 10, 15, 20, 25, 50, 75, 120, or more consecutivenucleotides of the displaced portion of the double-stranded nucleicacid.
 69. The method of claim 64, wherein the probe is complementary to100, 120, or more consecutive nucleotides of the displaced portion ofthe double-stranded nucleic acid.
 70. (canceled)
 71. A method ofselectively sequencing a plurality of different double-stranded nucleicacids in a sample according to a method of claim 48, wherein a pluralityof different probe oligonucleotides are utilized during the hybridizingstep.
 72. (canceled)
 73. A method of sequencing a double strandednucleic acid comprising one or more methylated cytosines, the methodcomprising: (a) ligating a first adapter to a first end of the doublestranded nucleic acid, and ligating a second adapter to a second end ofthe double stranded nucleic acid, wherein the second adapter is ahairpin adapter, thereby forming a nucleic acid template; (b) convertingone or more cytosines to uracil; (c) annealing a first primer to thenucleic acid template, wherein the first primer comprises a sequencethat is complementary to a portion of the first adapter, or a complementthereof; (d) sequencing a first portion of the nucleic acid template byextending the first primer, thereby generating a first read comprising afirst nucleic acid sequence of at least a first portion of the doublestranded nucleic acid; (e) annealing a second primer to the nucleic acidtemplate, wherein the second primer comprises a sequence that iscomplementary to a sequence within a loop of the hairpin adapter, or acomplement thereof; and (f) sequencing a second portion of the nucleicacid template by extending the second primer, thereby generating asecond read comprising a nucleic acid sequence of at least a secondportion of the double stranded nucleic acid. 74-79. (canceled)
 80. Amethod of sequencing a first portion and a second portion of adouble-stranded nucleic acid, the method comprising: a. ligating a firstadapter to a first end of the double stranded nucleic acid, and ligatinga second adapter to a second end of the double stranded nucleic acid,wherein the second adapter is a hairpin adapter, thereby forming anucleic acid template; b. displacing at least a portion of one strand ofthe nucleic acid template by annealing a blocking primer to the nucleicacid template and extending the blocking primer to generate a blockingstrand, wherein the blocking primer comprises a sequence within a loopof the hairpin adapter, or a complement thereof; c. annealing a firstsequencing primer to the nucleic acid template and sequencing a firstportion of the nucleic acid template by extending the first sequencingprimer, thereby generating a first read comprising a first nucleic acidsequence of at least a first portion of the double stranded nucleicacid, wherein the first sequencing primer comprises a sequence that iscomplementary to a portion of the first adapter; and d. annealing asecond sequencing primer to the nucleic acid template and sequencing asecond portion of the nucleic acid template by extending the secondsequencing primer, thereby generating a second read comprising a secondnucleic acid sequence of at least a second portion of the doublestranded nucleic acid, wherein the second sequencing primer comprises asequence that is complementary to a sequence within a loop of thehairpin adapter, or a complement thereof. 81-84. (canceled)